Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 10:59:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zk9_11241/04_2023/6zk9_11241_neut_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.009 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 13 5.49 5 S 188 5.16 5 C 17801 2.51 5 N 4889 2.21 5 O 6666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29587 Number of models: 1 Model: "" Number of chains: 45 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3047 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 245 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 4, 'TRANS': 26} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "2" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "3" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 285 Classifications: {'water': 285} Link IDs: {None: 284} Chain: "4" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 200 Classifications: {'water': 200} Link IDs: {None: 199} Chain: "5" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "6" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "9" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "a" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "b" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "c" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "d" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "e" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "g" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "h" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 76.543 53.579 111.864 1.00 35.70 S ATOM 2695 SG CYS 1 362 78.851 53.632 106.580 1.00 50.14 S ATOM 2676 SG CYS 1 359 83.775 53.674 112.497 1.00 52.93 S ATOM 3039 SG CYS 1 405 80.358 47.743 110.807 1.00 47.41 S ATOM 4116 SG CYS 2 103 74.552 48.610 130.636 1.00 57.20 S ATOM 4150 SG CYS 2 108 72.542 46.250 132.831 1.00 60.11 S ATOM 4430 SG CYS 2 144 76.031 44.903 127.052 1.00 71.98 S ATOM 4453 SG CYS 2 148 74.232 42.140 128.574 1.00 58.51 S ATOM 5793 SG CYS 3 114 79.009 71.894 97.053 1.00 42.51 S ATOM 5732 SG CYS 3 105 73.856 75.366 99.064 1.00 46.29 S ATOM 5753 SG CYS 3 108 80.029 76.829 100.879 1.00 31.92 S ATOM 6125 SG CYS 3 156 86.138 64.291 101.677 1.00 37.88 S ATOM 6102 SG CYS 3 153 84.204 67.270 107.389 1.00 38.57 S ATOM 6149 SG CYS 3 159 90.259 67.901 105.566 1.00 72.59 S ATOM 6479 SG CYS 3 203 86.185 70.521 101.877 1.00 35.52 S ATOM 5238 SG CYS 3 41 85.169 57.774 99.890 1.00 33.03 S ATOM 5324 SG CYS 3 52 81.457 58.986 98.931 1.00 42.22 S ATOM 5349 SG CYS 3 55 81.828 53.979 95.600 1.00 37.68 S ATOM 5450 SG CYS 3 69 85.456 54.021 96.936 1.00 41.26 S ATOM 15270 SG CYS 6 55 58.249 101.716 76.827 1.00 60.47 S ATOM 15768 SG CYS 6 119 64.232 97.547 74.960 1.00 60.54 S ATOM 15998 SG CYS 6 149 61.254 95.551 79.932 1.00 43.23 S ATOM 15264 SG CYS 6 54 57.455 95.447 74.102 1.00 92.29 S ATOM 17190 SG CYS 9 116 65.210 96.301 86.227 1.00 54.58 S ATOM 17237 SG CYS 9 122 65.787 91.834 91.009 1.00 37.48 S ATOM 16964 SG CYS 9 87 69.661 91.531 85.677 1.00 32.10 S ATOM 17266 SG CYS 9 126 67.930 88.448 98.200 1.00 25.33 S ATOM 16937 SG CYS 9 83 71.547 90.077 93.043 1.00 39.44 S ATOM 16895 SG CYS 9 77 73.752 91.612 98.861 1.00 32.31 S ATOM 16914 SG CYS 9 80 72.883 85.127 96.843 1.00 36.56 S ATOM 18513 SG CYS b 59 69.772 84.146 113.454 1.00 48.78 S ATOM 18691 SG CYS b 84 72.713 84.076 111.023 1.00 39.82 S ATOM 18713 SG CYS b 87 71.049 87.104 111.945 1.00 45.15 S Time building chain proxies: 17.22, per 1000 atoms: 0.58 Number of scatterers: 29587 At special positions: 0 Unit cell: (149, 159, 161.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 188 16.00 P 13 15.00 O 6666 8.00 N 4889 7.00 C 17801 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: 14.39 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 25 sheets defined 38.3% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 37 Processing helix chain '1' and resid 45 through 62 removed outlier: 3.625A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.645A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.703A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 184 through 187 Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 309 through 312 No H-bonds generated for 'chain '1' and resid 309 through 312' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.483A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 3.917A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER 1 391 " --> pdb=" O GLU 1 388 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.665A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.480A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.931A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.782A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 110 Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 33 removed outlier: 3.802A pdb=" N VAL 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 196 through 202 removed outlier: 3.712A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE 3 202 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 275 removed outlier: 5.276A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS 3 275 " --> pdb=" O TYR 3 271 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 308 removed outlier: 3.713A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 360 through 362 No H-bonds generated for 'chain '3' and resid 360 through 362' Processing helix chain '3' and resid 369 through 373 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 432 removed outlier: 3.944A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.731A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 566 through 568 No H-bonds generated for 'chain '3' and resid 566 through 568' Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 631 removed outlier: 3.909A pdb=" N VAL 3 631 " --> pdb=" O PRO 3 628 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 628 through 631' Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 87 through 93 removed outlier: 4.216A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 102 Proline residue: 4 101 - end of helix Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.535A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 3.947A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.870A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 263 removed outlier: 4.636A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.705A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.038A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 3.635A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.873A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU 5 64 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG 5 65 " --> pdb=" O THR 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 138 removed outlier: 3.877A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE 5 138 " --> pdb=" O TRP 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 43 Processing helix chain '6' and resid 54 through 63 removed outlier: 3.531A pdb=" N GLU 6 58 " --> pdb=" O CYS 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 94 through 106 Proline residue: 6 98 - end of helix Processing helix chain '6' and resid 118 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.856A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 61 removed outlier: 4.662A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.629A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 45 removed outlier: 3.657A pdb=" N ALA b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 31 removed outlier: 4.226A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.543A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 3 through 5 No H-bonds generated for 'chain 'd' and resid 3 through 5' Processing helix chain 'd' and resid 29 through 39 removed outlier: 3.919A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 5.150A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 301 through 303 No H-bonds generated for 'chain 'd' and resid 301 through 303' Processing helix chain 'd' and resid 310 through 321 removed outlier: 5.128A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 46 removed outlier: 4.865A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS e 38 " --> pdb=" O PHE e 35 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG e 39 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR e 40 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL e 41 " --> pdb=" O LYS e 38 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU e 42 " --> pdb=" O ARG e 39 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS e 45 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.134A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 64 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.811A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 3.956A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.431A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'i' and resid 3 through 16 Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 3.631A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 82 Processing helix chain 'q' and resid 31 through 34 No H-bonds generated for 'chain 'q' and resid 31 through 34' Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.961A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 266 through 271 Processing sheet with id= C, first strand: chain '2' and resid 137 through 142 removed outlier: 6.542A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 Processing sheet with id= H, first strand: chain '3' and resid 283 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.572A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 490 through 493 removed outlier: 8.090A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 572 through 574 Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.678A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 172 through 177 Processing sheet with id= P, first strand: chain '6' and resid 47 through 51 removed outlier: 6.251A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '9' and resid 65 through 67 Processing sheet with id= R, first strand: chain '9' and resid 92 through 98 removed outlier: 6.012A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= T, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= U, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= V, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= W, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.430A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.872A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.469A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) 871 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.38 Time building geometry restraints manager: 15.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 12001 1.43 - 1.67: 16418 1.67 - 1.90: 255 1.90 - 2.14: 0 2.14 - 2.37: 80 Bond restraints: 28754 Sorted by residual: bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.487 1.339 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.474 1.327 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C10 ZMP g 201 " pdb=" S1 ZMP g 201 " ideal model delta sigma weight residual 1.852 1.711 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.591 0.242 3.80e-02 6.93e+02 4.05e+01 bond pdb=" OA3 CDL h 201 " pdb=" PA1 CDL h 201 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.00e-02 1.00e+04 3.61e+01 ... (remaining 28749 not shown) Histogram of bond angle deviations from ideal: 62.33 - 76.69: 73 76.69 - 91.05: 7 91.05 - 105.41: 815 105.41 - 119.76: 24631 119.76 - 134.12: 13393 Bond angle restraints: 38919 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 73.86 46.74 3.00e+00 1.11e-01 2.43e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 70.25 39.05 3.00e+00 1.11e-01 1.69e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.45 -23.71 1.95e+00 2.62e-01 1.47e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.90 13.43 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.85 13.48 1.20e+00 6.94e-01 1.26e+02 ... (remaining 38914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 17225 34.41 - 68.82: 136 68.82 - 103.22: 14 103.22 - 137.63: 1 137.63 - 172.04: 1 Dihedral angle restraints: 17377 sinusoidal: 7331 harmonic: 10046 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -130.85 -49.15 0 5.00e+00 4.00e-02 9.66e+01 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" C10 FMN 1 502 " pdb=" C1' FMN 1 502 " pdb=" N10 FMN 1 502 " pdb=" C2' FMN 1 502 " ideal model delta sinusoidal sigma weight residual 257.59 85.55 172.04 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 17374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.237: 4192 4.237 - 8.475: 0 8.475 - 12.712: 0 12.712 - 16.950: 0 16.950 - 21.187: 24 Chirality restraints: 4216 Sorted by residual: chirality pdb="FE1 SF4 9 403 " pdb=" S2 SF4 9 403 " pdb=" S3 SF4 9 403 " pdb=" S4 SF4 9 403 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 4213 not shown) Planarity restraints: 4994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.039 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR 6 125 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.019 2.00e-02 2.50e+03 3.32e-02 2.20e+01 pdb=" CG TYR 9 40 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 371 " 0.026 2.00e-02 2.50e+03 2.46e-02 1.51e+01 pdb=" CG TRP 1 371 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 371 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 371 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 371 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 371 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 371 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 371 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 371 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 371 " 0.001 2.00e-02 2.50e+03 ... (remaining 4991 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.83: 10167 2.83 - 3.41: 33734 3.41 - 3.99: 69173 3.99 - 4.56: 92670 4.56 - 5.14: 131118 Nonbonded interactions: 336862 Sorted by model distance: nonbonded pdb=" OD2 ASP 5 77 " pdb=" OG1 THR 5 79 " model vdw 2.257 2.440 nonbonded pdb=" OH TYR d 33 " pdb=" O HOH d 501 " model vdw 2.260 2.440 nonbonded pdb=" O PHE 4 141 " pdb=" OG1 THR 4 145 " model vdw 2.269 2.440 nonbonded pdb=" O ILE 9 94 " pdb=" O HOH 9 501 " model vdw 2.276 2.440 nonbonded pdb=" OG SER 5 119 " pdb=" OE2 GLU 5 131 " model vdw 2.278 2.440 ... (remaining 336857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.560 Check model and map are aligned: 0.450 Set scattering table: 0.250 Process input model: 89.320 Find NCS groups from input model: 0.900 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.242 28754 Z= 0.539 Angle : 1.052 46.737 38919 Z= 0.572 Chirality : 1.582 21.187 4216 Planarity : 0.008 0.062 4994 Dihedral : 10.466 172.040 10913 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.12), residues: 3430 helix: -2.26 (0.10), residues: 1325 sheet: -1.27 (0.23), residues: 366 loop : -1.15 (0.13), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 639 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 5 residues processed: 641 average time/residue: 1.9041 time to fit residues: 1386.0175 Evaluate side-chains 461 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 456 time to evaluate : 3.593 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 3 average time/residue: 0.4243 time to fit residues: 6.9009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 10.0000 chunk 257 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 308 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN 1 356 HIS 1 373 ASN 3 179 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 232 ASN 4 252 ASN 4 313 GLN 5 211 GLN 6 106 GLN 6 162 GLN 9 6 ASN 9 65 HIS a 35 ASN a 40 ASN a 55 ASN b 36 ASN b 74 ASN c 67 ASN d 115 GLN d 184 ASN e 92 ASN f 49 GLN f 75 GLN f 95 GLN g 125 HIS h 28 GLN i 69 ASN i 122 GLN i 123 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.273 28754 Z= 0.789 Angle : 2.322 50.788 38919 Z= 1.531 Chirality : 0.479 6.484 4216 Planarity : 0.005 0.046 4994 Dihedral : 8.393 172.364 4053 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3430 helix: -0.57 (0.13), residues: 1320 sheet: -0.94 (0.23), residues: 388 loop : -0.56 (0.14), residues: 1722 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 460 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 14 residues processed: 481 average time/residue: 1.9061 time to fit residues: 1044.5039 Evaluate side-chains 451 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 437 time to evaluate : 3.755 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 9 average time/residue: 0.7959 time to fit residues: 14.9372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 309 optimal weight: 0.8980 chunk 334 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 444 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 144 ASN 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 234 ASN d 296 HIS e 30 GLN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.243 28754 Z= 0.773 Angle : 2.323 50.659 38919 Z= 1.531 Chirality : 0.484 6.567 4216 Planarity : 0.005 0.051 4994 Dihedral : 8.250 173.741 4053 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3430 helix: 0.17 (0.14), residues: 1333 sheet: -0.69 (0.24), residues: 393 loop : -0.21 (0.15), residues: 1704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 447 time to evaluate : 3.716 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 21 residues processed: 478 average time/residue: 1.7956 time to fit residues: 981.5763 Evaluate side-chains 451 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 430 time to evaluate : 3.956 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.6349 time to fit residues: 13.6236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 0.9990 chunk 232 optimal weight: 0.0060 chunk 160 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 237 ASN 3 444 GLN 3 461 ASN 3 581 GLN ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN a 40 ASN d 184 ASN d 234 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN h 28 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.245 28754 Z= 0.752 Angle : 2.313 50.608 38919 Z= 1.527 Chirality : 0.481 6.470 4216 Planarity : 0.004 0.041 4994 Dihedral : 7.996 172.417 4053 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3430 helix: 0.51 (0.14), residues: 1326 sheet: -0.64 (0.24), residues: 372 loop : -0.01 (0.15), residues: 1732 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 446 time to evaluate : 3.819 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 20 residues processed: 476 average time/residue: 1.8135 time to fit residues: 992.1724 Evaluate side-chains 456 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 436 time to evaluate : 3.819 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.5637 time to fit residues: 10.8118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 280 optimal weight: 0.0020 chunk 227 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 167 optimal weight: 9.9990 chunk 294 optimal weight: 0.1980 chunk 82 optimal weight: 9.9990 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 373 ASN 3 444 GLN 3 461 ASN 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 234 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.246 28754 Z= 0.749 Angle : 2.308 50.587 38919 Z= 1.525 Chirality : 0.479 6.428 4216 Planarity : 0.004 0.040 4994 Dihedral : 7.741 171.006 4053 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3430 helix: 0.71 (0.14), residues: 1323 sheet: -0.59 (0.25), residues: 374 loop : 0.10 (0.15), residues: 1733 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 432 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 461 average time/residue: 1.8591 time to fit residues: 986.4981 Evaluate side-chains 448 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 428 time to evaluate : 3.895 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.6434 time to fit residues: 10.5246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 328 optimal weight: 9.9990 chunk 273 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 437 HIS 3 444 GLN 3 459 GLN ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN a 40 ASN d 36 ASN d 184 ASN d 234 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.243 28754 Z= 0.807 Angle : 2.331 50.640 38919 Z= 1.534 Chirality : 0.485 6.616 4216 Planarity : 0.005 0.079 4994 Dihedral : 8.082 174.078 4053 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3430 helix: 0.66 (0.14), residues: 1339 sheet: -0.43 (0.24), residues: 387 loop : 0.12 (0.15), residues: 1704 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 432 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 29 residues processed: 462 average time/residue: 1.8767 time to fit residues: 990.2973 Evaluate side-chains 449 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 420 time to evaluate : 4.096 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 17 residues processed: 12 average time/residue: 0.5976 time to fit residues: 14.8124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 276 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 327 optimal weight: 0.0980 chunk 205 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 16 GLN 3 444 GLN ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 234 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.244 28754 Z= 0.755 Angle : 2.314 50.581 38919 Z= 1.527 Chirality : 0.482 6.484 4216 Planarity : 0.004 0.037 4994 Dihedral : 7.845 172.124 4053 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3430 helix: 0.79 (0.14), residues: 1331 sheet: -0.49 (0.25), residues: 369 loop : 0.20 (0.15), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 432 time to evaluate : 4.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 22 residues processed: 456 average time/residue: 1.7883 time to fit residues: 931.3768 Evaluate side-chains 448 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 426 time to evaluate : 2.771 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.6438 time to fit residues: 7.0685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 195 optimal weight: 0.4980 chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 GLN 3 461 ASN ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 234 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.242 28754 Z= 0.777 Angle : 2.322 50.586 38919 Z= 1.530 Chirality : 0.484 6.555 4216 Planarity : 0.004 0.056 4994 Dihedral : 7.930 173.051 4053 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3430 helix: 0.76 (0.14), residues: 1336 sheet: -0.40 (0.24), residues: 385 loop : 0.20 (0.15), residues: 1709 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 428 time to evaluate : 4.408 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 28 residues processed: 454 average time/residue: 1.8573 time to fit residues: 968.3868 Evaluate side-chains 455 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 427 time to evaluate : 3.662 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 10 average time/residue: 0.8080 time to fit residues: 15.4416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 305 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 275 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 304 optimal weight: 0.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 16 GLN 3 444 GLN 3 461 ASN ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 234 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.244 28754 Z= 0.761 Angle : 2.317 50.594 38919 Z= 1.528 Chirality : 0.482 6.497 4216 Planarity : 0.004 0.037 4994 Dihedral : 7.826 172.393 4053 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3430 helix: 0.82 (0.14), residues: 1333 sheet: -0.43 (0.24), residues: 386 loop : 0.27 (0.15), residues: 1711 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 430 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 454 average time/residue: 1.8655 time to fit residues: 973.8416 Evaluate side-chains 450 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 425 time to evaluate : 3.494 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 7 average time/residue: 0.5987 time to fit residues: 10.8328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 10.0000 chunk 322 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 311 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 16 GLN 3 119 GLN 3 444 GLN 3 461 ASN ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN a 40 ASN d 184 ASN d 234 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN i 91 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.238 28754 Z= 0.820 Angle : 2.335 50.609 38919 Z= 1.534 Chirality : 0.488 6.640 4216 Planarity : 0.005 0.083 4994 Dihedral : 8.144 174.251 4053 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3430 helix: 0.69 (0.14), residues: 1333 sheet: -0.30 (0.25), residues: 376 loop : 0.21 (0.15), residues: 1721 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 425 time to evaluate : 3.611 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 445 average time/residue: 1.9021 time to fit residues: 969.5861 Evaluate side-chains 437 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 414 time to evaluate : 3.715 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.4237 time to fit residues: 7.5331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 6.9990 chunk 287 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 16 GLN 3 444 GLN 3 461 ASN ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.072195 restraints weight = 23601.242| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.05 r_work: 0.2755 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 28754 Z= 0.780 Angle : 2.326 50.586 38919 Z= 1.532 Chirality : 0.485 6.569 4216 Planarity : 0.004 0.054 4994 Dihedral : 8.067 173.539 4053 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3430 helix: 0.71 (0.14), residues: 1333 sheet: -0.41 (0.24), residues: 386 loop : 0.23 (0.15), residues: 1711 =============================================================================== Job complete usr+sys time: 15023.05 seconds wall clock time: 266 minutes 18.92 seconds (15978.92 seconds total)