Starting phenix.real_space_refine on Sun Mar 24 18:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oa1_3727/03_2024/5oa1_3727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oa1_3727/03_2024/5oa1_3727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oa1_3727/03_2024/5oa1_3727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oa1_3727/03_2024/5oa1_3727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oa1_3727/03_2024/5oa1_3727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oa1_3727/03_2024/5oa1_3727.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 105 5.49 5 S 193 5.16 5 C 26700 2.51 5 N 7806 2.21 5 O 8648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A GLU 994": "OE1" <-> "OE2" Residue "A TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1008": "OD1" <-> "OD2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B TYR 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 965": "OE1" <-> "OE2" Residue "B TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43459 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 11513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1458, 11513 Classifications: {'peptide': 1458} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1398} Chain breaks: 9 Chain: "B" Number of atoms: 9327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9327 Classifications: {'peptide': 1175} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1115} Chain breaks: 2 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: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 119} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 831 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3811 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1028 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "T" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1128 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "U" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 1164 Classifications: {'peptide': 291} Incomplete info: {'backbone_only': 283} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 8 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1307 Unresolved non-hydrogen angles: 1874 Unresolved non-hydrogen dihedrals: 871 Unresolved non-hydrogen chiralities: 379 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 9, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 10, 'PHE:plan': 12, 'GLU:plan': 16, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 588 Chain: "V" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 1152 Classifications: {'peptide': 288} Incomplete info: {'backbone_only': 274} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain breaks: 3 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1234 Unresolved non-hydrogen angles: 1792 Unresolved non-hydrogen dihedrals: 793 Unresolved non-hydrogen chiralities: 371 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 20, 'PHE:plan': 14, 'GLU:plan': 14, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 611 Chain: "W" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 672 Classifications: {'peptide': 168} Incomplete info: {'backbone_only': 165} Link IDs: {'TRANS': 167} Chain breaks: 7 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 1108 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 6, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 384 Chain: "1" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 52 Classifications: {'peptide': 13} Incomplete info: {'backbone_only': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 76 Classifications: {'peptide': 19} Incomplete info: {'backbone_only': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen chiralities: 19 Chain: "3" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 36 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "4" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 92 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen chiralities: 23 Chain: "5" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 64 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "6" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 40 Classifications: {'peptide': 10} Incomplete info: {'backbone_only': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "7" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 100 Classifications: {'peptide': 25} Incomplete info: {'backbone_only': 25} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen chiralities: 25 Chain: "8" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 40 Classifications: {'peptide': 10} Incomplete info: {'backbone_only': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "9" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 36 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 64 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 16} Link IDs: {'TRANS': 15} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "P" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 88 Classifications: {'peptide': 22} Incomplete info: {'backbone_only': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen chiralities: 22 Chain: "Z" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 60 Classifications: {'peptide': 15} Incomplete info: {'backbone_only': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "Y" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 48 Classifications: {'peptide': 12} Incomplete info: {'backbone_only': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 108 Classifications: {'peptide': 27} Incomplete info: {'backbone_only': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen chiralities: 27 Chain: "A" 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: "B" 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 781 SG CYS A 102 133.009 51.455 76.703 1.00108.95 S ATOM 806 SG CYS A 105 131.957 48.185 75.238 1.00111.29 S ATOM 1605 SG CYS A 233 132.833 48.299 78.974 1.00112.17 S ATOM 1627 SG CYS A 236 135.518 48.791 75.920 1.00124.79 S ATOM 461 SG CYS A 62 89.436 71.280 58.000 1.00 94.92 S ATOM 480 SG CYS A 65 86.647 68.841 58.490 1.00 92.34 S ATOM 535 SG CYS A 72 87.444 70.978 61.201 1.00 92.92 S ATOM 20128 SG CYS B1104 92.582 53.653 62.185 1.00 81.64 S ATOM 20154 SG CYS B1107 95.298 55.126 63.877 1.00 88.74 S ATOM 20301 SG CYS B1128 93.955 56.840 60.906 1.00 84.61 S ATOM 20329 SG CYS B1131 95.842 53.421 60.578 1.00 88.47 S ATOM 29064 SG CYS I 13 143.994 103.105 130.171 1.00161.37 S ATOM 29184 SG CYS I 30 146.200 100.497 128.678 1.00194.69 S ATOM 29975 SG CYS J 7 48.793 97.109 115.131 1.00101.98 S ATOM 29998 SG CYS J 10 44.893 95.822 115.263 1.00 97.69 S ATOM 30278 SG CYS J 45 47.767 95.180 118.171 1.00101.16 S ATOM 30284 SG CYS J 46 45.993 98.307 117.324 1.00101.59 S ATOM 31350 SG CYS L 31 73.249 123.402 89.026 1.00125.00 S ATOM 31370 SG CYS L 34 71.757 126.608 89.663 1.00127.07 S ATOM 31474 SG CYS L 48 72.648 125.910 86.175 1.00139.22 S ATOM 31497 SG CYS L 51 75.342 126.655 89.646 1.00135.61 S Residues with excluded nonbonded symmetry interactions: 60 residue: pdb=" P DG S 7 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG S 7 " occ=0.00 residue: pdb=" P DT S 8 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT S 8 " occ=0.00 residue: pdb=" P DC S 9 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC S 9 " occ=0.00 residue: pdb=" P DA S 10 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA S 10 " occ=0.00 residue: pdb=" P DT S 11 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT S 11 " occ=0.00 residue: pdb=" P DG S 12 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG S 12 " occ=0.00 residue: pdb=" P DG S 13 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG S 13 " occ=0.00 residue: pdb=" P DA S 14 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA S 14 " occ=0.00 residue: pdb=" P DG S 15 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG S 15 " occ=0.00 residue: pdb=" P DT S 16 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT S 16 " occ=0.00 residue: pdb=" P DA S 17 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA S 17 " occ=0.00 residue: pdb=" P DC S 18 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC S 18 " occ=0.00 ... (remaining 48 not shown) Time building chain proxies: 20.50, per 1000 atoms: 0.47 Number of scatterers: 43459 At special positions: 0 Unit cell: (167.4, 210.6, 179.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 193 16.00 P 105 15.00 O 8648 8.00 N 7806 7.00 C 26700 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: 16.69 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " 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 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 27 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8858 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 58 sheets defined 44.7% alpha, 17.4% beta 33 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 15.49 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.707A pdb=" N SER A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.645A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.664A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.875A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.917A pdb=" N PHE A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.665A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.101A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 380 through 400 removed outlier: 4.161A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.549A pdb=" N LYS A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.737A pdb=" N GLN A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.521A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.508A pdb=" N THR A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 571 " --> pdb=" O VAL A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.614A pdb=" N SER A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR A 657 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.589A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.780A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 862 removed outlier: 3.666A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.550A pdb=" N ILE A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.586A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.579A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 removed outlier: 3.677A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.563A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.659A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1176 removed outlier: 3.607A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 3.586A pdb=" N VAL A1266 " --> pdb=" O LEU A1262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1262 through 1266' Processing helix chain 'A' and resid 1298 through 1306 Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.525A pdb=" N VAL A1316 " --> pdb=" O GLU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1338 Processing helix chain 'A' and resid 1440 through 1452 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.719A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.609A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.988A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.677A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1629 Processing helix chain 'A' and resid 1636 through 1644 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.010A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.631A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 59 " --> pdb=" O PRO B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.664A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 4.142A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.718A pdb=" N LEU B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.553A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.528A pdb=" N MET B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.794A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.094A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.842A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.696A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.005A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 removed outlier: 3.531A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 725 removed outlier: 3.523A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.570A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.541A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.804A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1136 through 1138 No H-bonds generated for 'chain 'B' and resid 1136 through 1138' Processing helix chain 'B' and resid 1180 through 1192 Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.643A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.561A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.903A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.500A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.972A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.541A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.655A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.590A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.646A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.623A pdb=" N SER E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.518A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.558A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.666A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 10 through 20 removed outlier: 3.943A pdb=" N ARG G 15 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.939A pdb=" N ASN H 131 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 132' Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.954A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.050A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.977A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'O' and resid 49 through 65 removed outlier: 3.531A pdb=" N SER O 53 " --> pdb=" O ALA O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 80 removed outlier: 3.637A pdb=" N LEU O 80 " --> pdb=" O ASN O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 103 removed outlier: 3.788A pdb=" N ASN O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 107 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 124 through 128 Processing helix chain 'O' and resid 129 through 147 removed outlier: 3.727A pdb=" N SER O 146 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.579A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 164 No H-bonds generated for 'chain 'O' and resid 162 through 164' Processing helix chain 'O' and resid 169 through 183 Processing helix chain 'O' and resid 186 through 197 Processing helix chain 'O' and resid 204 through 220 removed outlier: 3.685A pdb=" N LEU O 215 " --> pdb=" O TYR O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 247 Processing helix chain 'O' and resid 325 through 347 removed outlier: 3.554A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 354 Processing helix chain 'O' and resid 356 through 373 Processing helix chain 'O' and resid 381 through 390 removed outlier: 4.222A pdb=" N MET O 385 " --> pdb=" O ILE O 381 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN O 390 " --> pdb=" O PHE O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 408 removed outlier: 3.828A pdb=" N PHE O 408 " --> pdb=" O ILE O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 431 removed outlier: 3.668A pdb=" N ILE O 418 " --> pdb=" O ALA O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 456 removed outlier: 3.625A pdb=" N ILE O 439 " --> pdb=" O SER O 435 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL O 442 " --> pdb=" O GLN O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 466 through 469 Processing helix chain 'O' and resid 470 through 488 Processing helix chain 'O' and resid 489 through 491 No H-bonds generated for 'chain 'O' and resid 489 through 491' Processing helix chain 'O' and resid 498 through 500 No H-bonds generated for 'chain 'O' and resid 498 through 500' Processing helix chain 'O' and resid 501 through 511 removed outlier: 3.877A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET O 509 " --> pdb=" O PHE O 505 " (cutoff:3.500A) Processing helix chain 'O' and resid 515 through 520 removed outlier: 3.862A pdb=" N PHE O 519 " --> pdb=" O ASN O 515 " (cutoff:3.500A) Processing helix chain 'O' and resid 523 through 535 Processing helix chain 'O' and resid 540 through 551 Processing helix chain 'O' and resid 582 through 589 Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 608 through 610 No H-bonds generated for 'chain 'O' and resid 608 through 610' Processing helix chain 'U' and resid 97 through 124 removed outlier: 3.526A pdb=" N GLN U 115 " --> pdb=" O ILE U 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG U 124 " --> pdb=" O ILE U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 147 removed outlier: 3.576A pdb=" N HIS U 131 " --> pdb=" O LYS U 127 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU U 138 " --> pdb=" O LYS U 134 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS U 142 " --> pdb=" O LEU U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 173 removed outlier: 3.596A pdb=" N THR U 161 " --> pdb=" O HIS U 157 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 187 removed outlier: 3.503A pdb=" N LYS U 183 " --> pdb=" O CYS U 179 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP U 184 " --> pdb=" O ASP U 180 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 207 removed outlier: 3.747A pdb=" N GLN U 206 " --> pdb=" O SER U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 217 Processing helix chain 'U' and resid 227 through 237 removed outlier: 4.654A pdb=" N ALA U 231 " --> pdb=" O TYR U 227 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS U 234 " --> pdb=" O ILE U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 261 removed outlier: 4.270A pdb=" N LEU U 254 " --> pdb=" O GLN U 250 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS U 255 " --> pdb=" O GLY U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 281 Processing helix chain 'U' and resid 301 through 316 Processing helix chain 'U' and resid 405 through 417 removed outlier: 4.019A pdb=" N ALA U 409 " --> pdb=" O ASP U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 448 removed outlier: 3.545A pdb=" N GLU U 440 " --> pdb=" O LEU U 436 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 492 Processing helix chain 'U' and resid 495 through 514 removed outlier: 3.673A pdb=" N ASP U 500 " --> pdb=" O GLU U 496 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS U 501 " --> pdb=" O GLN U 497 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 226 removed outlier: 3.927A pdb=" N ARG W 211 " --> pdb=" O ASN W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 241 removed outlier: 4.288A pdb=" N ARG W 241 " --> pdb=" O ALA W 237 " (cutoff:3.500A) Processing helix chain 'W' and resid 251 through 261 Processing helix chain 'W' and resid 269 through 278 removed outlier: 3.758A pdb=" N TRP W 273 " --> pdb=" O ASP W 269 " (cutoff:3.500A) Processing helix chain 'W' and resid 308 through 321 removed outlier: 3.975A pdb=" N TYR W 312 " --> pdb=" O PHE W 308 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP W 314 " --> pdb=" O ILE W 310 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU W 317 " --> pdb=" O LEU W 313 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 353 removed outlier: 4.061A pdb=" N LEU W 342 " --> pdb=" O GLU W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 364 through 385 removed outlier: 3.665A pdb=" N LYS W 375 " --> pdb=" O CYS W 371 " (cutoff:3.500A) Processing helix chain 'W' and resid 401 through 420 removed outlier: 3.526A pdb=" N ILE W 417 " --> pdb=" O THR W 413 " (cutoff:3.500A) Processing helix chain 'W' and resid 430 through 442 Processing helix chain '1' and resid 10 through 21 Processing helix chain '2' and resid 3 through 20 Processing helix chain '3' and resid 16 through 23 Processing helix chain '4' and resid 3 through 24 Processing helix chain '5' and resid 28 through 42 Processing helix chain '6' and resid 44 through 52 Processing helix chain '7' and resid 54 through 77 Processing helix chain '8' and resid 79 through 87 Processing helix chain '9' and resid 89 through 96 Processing helix chain 'Q' and resid 98 through 103 Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'P' and resid 115 through 135 Processing helix chain 'Z' and resid 137 through 150 Processing helix chain 'Y' and resid 152 through 162 Processing helix chain 'R' and resid 164 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 6.826A pdb=" N ASN B1199 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 14 " --> pdb=" O ARG B1197 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG B1197 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE A 16 " --> pdb=" O ARG B1195 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG B1195 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 86 removed outlier: 6.319A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.781A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.863A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.708A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 752 removed outlier: 3.657A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.562A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.562A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB4, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.799A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 4.169A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1459 through 1462 removed outlier: 3.675A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.900A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.066A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 70 through 71 removed outlier: 4.207A pdb=" N GLU B 100 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS B 106 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG B 134 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 145 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 70 through 71 removed outlier: 4.207A pdb=" N GLU B 100 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS B 106 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG B 134 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.444A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.775A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC6, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC7, first strand: chain 'B' and resid 571 through 572 removed outlier: 7.044A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 740 through 744 removed outlier: 6.069A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 740 through 744 removed outlier: 6.069A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD2, first strand: chain 'B' and resid 857 through 863 removed outlier: 3.556A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD4, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD5, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD6, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD7, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.541A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N LEU C 291 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N ILE C 235 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ARG C 293 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE C 233 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG C 295 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N HIS C 297 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU C 229 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 299 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR C 227 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.359A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE L 67 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 85 " --> pdb=" O VAL L 65 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.768A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.365A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.520A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 132 through 140 removed outlier: 5.917A pdb=" N ILE G 137 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU G 148 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 139 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS G 158 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.521A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'I' and resid 82 through 83 Processing sheet with id=AF2, first strand: chain 'I' and resid 98 through 99 removed outlier: 3.990A pdb=" N LEU I 99 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR I 109 " --> pdb=" O LEU I 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'N' and resid 69 through 71 removed outlier: 6.766A pdb=" N ILE M 88 " --> pdb=" O ILE M 10 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN M 16 " --> pdb=" O LYS M 92 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 29 through 31 removed outlier: 6.986A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 21 through 23 Processing sheet with id=AF7, first strand: chain 'V' and resid 10 through 17 removed outlier: 4.025A pdb=" N ASP V 10 " --> pdb=" O SER V 553 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR V 549 " --> pdb=" O SER V 14 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU V 16 " --> pdb=" O VAL V 547 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL V 547 " --> pdb=" O LEU V 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR V 513 " --> pdb=" O LEU V 541 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 181 through 184 removed outlier: 3.530A pdb=" N ARG V 181 " --> pdb=" O TYR V 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR V 234 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 244 through 246 removed outlier: 5.954A pdb=" N ARG V 273 " --> pdb=" O PRO V 291 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 302 through 307 removed outlier: 3.723A pdb=" N ASP V 304 " --> pdb=" O ILE V 318 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TRP V 324 " --> pdb=" O THR V 350 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR V 350 " --> pdb=" O TRP V 324 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE V 326 " --> pdb=" O HIS V 348 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 360 through 365 removed outlier: 3.517A pdb=" N LYS V 379 " --> pdb=" O ASP V 376 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP V 384 " --> pdb=" O TRP V 389 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TRP V 389 " --> pdb=" O ASP V 384 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 404 through 407 Processing sheet with id=AG4, first strand: chain 'V' and resid 448 through 453 removed outlier: 3.548A pdb=" N ARG V 450 " --> pdb=" O SER V 470 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY V 503 " --> pdb=" O MET V 478 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL V 480 " --> pdb=" O PRO V 501 " (cutoff:3.500A) 2093 hydrogen bonds defined for protein. 5907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 26.19 Time building geometry restraints manager: 18.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.54: 40257 1.54 - 1.88: 4143 1.88 - 2.21: 0 2.21 - 2.55: 0 2.55 - 2.89: 12 Bond restraints: 44412 Sorted by residual: bond pdb=" C GLU V 355 " pdb=" N SER V 358 " ideal model delta sigma weight residual 1.332 2.834 -1.502 1.02e-02 9.61e+03 2.17e+04 bond pdb=" C PRO V 309 " pdb=" N ASP V 311 " ideal model delta sigma weight residual 1.331 2.803 -1.471 1.14e-02 7.69e+03 1.67e+04 bond pdb=" C PRO V 330 " pdb=" N ILE V 344 " ideal model delta sigma weight residual 1.335 2.772 -1.437 1.20e-02 6.94e+03 1.43e+04 bond pdb=" C SER V 427 " pdb=" N PRO V 432 " ideal model delta sigma weight residual 1.328 2.774 -1.446 1.25e-02 6.40e+03 1.34e+04 bond pdb=" C SER V 207 " pdb=" N LEU V 214 " ideal model delta sigma weight residual 1.332 2.886 -1.554 1.36e-02 5.41e+03 1.31e+04 ... (remaining 44407 not shown) Histogram of bond angle deviations from ideal: 64.90 - 83.50: 8 83.50 - 102.09: 250 102.09 - 120.68: 43360 120.68 - 139.28: 16382 139.28 - 157.87: 2 Bond angle restraints: 60002 Sorted by residual: angle pdb=" O SER V 207 " pdb=" C SER V 207 " pdb=" N LEU V 214 " ideal model delta sigma weight residual 123.27 64.90 58.37 1.16e+00 7.43e-01 2.53e+03 angle pdb=" O GLU V 355 " pdb=" C GLU V 355 " pdb=" N SER V 358 " ideal model delta sigma weight residual 122.08 78.20 43.88 1.07e+00 8.73e-01 1.68e+03 angle pdb=" CA SER V 207 " pdb=" C SER V 207 " pdb=" N LEU V 214 " ideal model delta sigma weight residual 116.39 72.13 44.26 1.17e+00 7.31e-01 1.43e+03 angle pdb=" O HIS V 483 " pdb=" C HIS V 483 " pdb=" N GLU V 499 " ideal model delta sigma weight residual 122.41 78.11 44.30 1.38e+00 5.25e-01 1.03e+03 angle pdb=" CA GLU V 355 " pdb=" C GLU V 355 " pdb=" N SER V 358 " ideal model delta sigma weight residual 116.79 81.83 34.96 1.28e+00 6.10e-01 7.46e+02 ... (remaining 59997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.43: 21579 18.43 - 36.86: 2332 36.86 - 55.29: 1042 55.29 - 73.72: 282 73.72 - 92.15: 101 Dihedral angle restraints: 25336 sinusoidal: 10708 harmonic: 14628 Sorted by residual: dihedral pdb=" CA LYS U 127 " pdb=" C LYS U 127 " pdb=" N GLU U 128 " pdb=" CA GLU U 128 " ideal model delta harmonic sigma weight residual 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU O 434 " pdb=" C LEU O 434 " pdb=" N SER O 435 " pdb=" CA SER O 435 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA SER O 448 " pdb=" C SER O 448 " pdb=" N TRP O 449 " pdb=" CA TRP O 449 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 25333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 6056 0.186 - 0.372: 99 0.372 - 0.557: 15 0.557 - 0.743: 3 0.743 - 0.929: 1 Chirality restraints: 6174 Sorted by residual: chirality pdb=" C1' DT T 42 " pdb=" O4' DT T 42 " pdb=" C2' DT T 42 " pdb=" N1 DT T 42 " both_signs ideal model delta sigma weight residual False 2.47 1.54 0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CG LEU O 180 " pdb=" CB LEU O 180 " pdb=" CD1 LEU O 180 " pdb=" CD2 LEU O 180 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C3' DC T 43 " pdb=" C4' DC T 43 " pdb=" O3' DC T 43 " pdb=" C2' DC T 43 " both_signs ideal model delta sigma weight residual False -2.66 -3.24 0.58 2.00e-01 2.50e+01 8.39e+00 ... (remaining 6171 not shown) Planarity restraints: 7686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS V 483 " -0.186 2.00e-02 2.50e+03 2.72e-01 7.38e+02 pdb=" C HIS V 483 " 0.446 2.00e-02 2.50e+03 pdb=" O HIS V 483 " -0.247 2.00e-02 2.50e+03 pdb=" N GLU V 499 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU V 355 " -0.190 2.00e-02 2.50e+03 2.63e-01 6.94e+02 pdb=" C GLU V 355 " 0.421 2.00e-02 2.50e+03 pdb=" O GLU V 355 " -0.253 2.00e-02 2.50e+03 pdb=" N SER V 358 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU V 442 " 0.155 2.00e-02 2.50e+03 2.38e-01 5.65e+02 pdb=" C LEU V 442 " -0.398 2.00e-02 2.50e+03 pdb=" O LEU V 442 " 0.205 2.00e-02 2.50e+03 pdb=" N ASP V 446 " 0.038 2.00e-02 2.50e+03 ... (remaining 7683 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.36: 37 1.36 - 2.24: 288 2.24 - 3.13: 30296 3.13 - 4.01: 116010 4.01 - 4.90: 201839 Warning: very small nonbonded interaction distances. Nonbonded interactions: 348470 Sorted by model distance: nonbonded pdb=" CD2 LEU B 898 " pdb=" CG2 VAL L 46 " model vdw 0.473 3.880 nonbonded pdb=" CG1 ILE G 139 " pdb=" OH TYR O 178 " model vdw 0.707 3.440 nonbonded pdb=" CD2 LEU B 95 " pdb=" CE1 PHE B 440 " model vdw 0.711 3.760 nonbonded pdb=" CG LEU B 95 " pdb=" CE2 PHE B 440 " model vdw 0.726 3.770 nonbonded pdb=" ND2 ASN G 154 " pdb=" C MET O 182 " model vdw 0.799 3.350 ... (remaining 348465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '1' and resid 10 through 21) selection = chain 'Y' selection = (chain 'Z' and resid 139 through 150) } ncs_group { reference = chain '2' selection = (chain 'P' and resid 117 through 135) } ncs_group { reference = chain '3' selection = (chain '6' and resid 44 through 52) selection = (chain '8' and resid 79 through 87) selection = chain '9' } ncs_group { reference = chain '4' selection = (chain '7' and resid 55 through 77) selection = (chain 'R' and resid 167 through 189) } ncs_group { reference = chain '5' selection = chain 'Q' } 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=0.00 max=1.00 mean=0.97 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: 1.280 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: 0.060 Extract box with map and model: 7.640 Check model and map are aligned: 0.690 Set scattering table: 0.370 Process input model: 137.290 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 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 : 0.027 1.554 44412 Z= 1.750 Angle : 1.757 58.365 60002 Z= 1.224 Chirality : 0.074 0.929 6174 Planarity : 0.009 0.272 7686 Dihedral : 19.192 92.151 16478 Min Nonbonded Distance : 0.473 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 1.18 % Allowed : 5.42 % Favored : 93.40 % Rotamer: Outliers : 8.67 % Allowed : 10.59 % Favored : 80.74 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.42 % Cis-general : 0.00 % 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: -1.92 (0.10), residues: 5498 helix: -0.78 (0.10), residues: 2196 sheet: -1.14 (0.17), residues: 729 loop : -1.69 (0.11), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP B 832 HIS 0.016 0.003 HIS B 646 PHE 0.037 0.004 PHE B1044 TYR 0.043 0.006 TYR A1174 ARG 0.009 0.001 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10996 Ramachandran restraints generated. 5498 Oldfield, 0 Emsley, 5498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1900 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1538 time to evaluate : 4.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 390 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5869 (mt) REVERT: A 485 SER cc_start: 0.9266 (m) cc_final: 0.8645 (p) REVERT: A 490 ILE cc_start: 0.9324 (pt) cc_final: 0.8801 (tt) REVERT: A 594 THR cc_start: 0.8338 (m) cc_final: 0.8010 (p) REVERT: A 597 LYS cc_start: 0.8943 (pttm) cc_final: 0.8712 (pttt) REVERT: A 600 MET cc_start: 0.7450 (ttt) cc_final: 0.6244 (ttt) REVERT: A 673 HIS cc_start: 0.7130 (m170) cc_final: 0.6596 (m170) REVERT: A 675 SER cc_start: 0.9452 (m) cc_final: 0.8976 (p) REVERT: A 690 GLU cc_start: 0.8126 (mp0) cc_final: 0.7843 (mp0) REVERT: A 822 THR cc_start: 0.9258 (m) cc_final: 0.8890 (p) REVERT: A 832 ASP cc_start: 0.8178 (m-30) cc_final: 0.7818 (m-30) REVERT: A 956 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7780 (mtt180) REVERT: A 977 MET cc_start: 0.7667 (ttt) cc_final: 0.6832 (ttt) REVERT: A 1032 VAL cc_start: 0.9169 (t) cc_final: 0.8890 (t) REVERT: A 1057 ILE cc_start: 0.8892 (mp) cc_final: 0.8668 (mt) REVERT: A 1080 TYR cc_start: 0.6800 (m-80) cc_final: 0.5931 (m-10) REVERT: A 1144 LEU cc_start: 0.9236 (tp) cc_final: 0.9025 (pp) REVERT: A 1190 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9023 (t) REVERT: A 1192 SER cc_start: 0.9219 (m) cc_final: 0.8859 (p) REVERT: A 1238 MET cc_start: 0.8106 (mtm) cc_final: 0.7589 (mtt) REVERT: A 1242 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 1434 GLU cc_start: 0.3664 (OUTLIER) cc_final: 0.2092 (pt0) REVERT: A 1530 TRP cc_start: 0.8727 (m-10) cc_final: 0.8506 (m-10) REVERT: A 1588 MET cc_start: 0.8229 (tpt) cc_final: 0.7861 (tpt) REVERT: A 1594 THR cc_start: 0.7437 (p) cc_final: 0.6834 (p) REVERT: B 21 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7773 (tpt170) REVERT: B 25 PHE cc_start: 0.8846 (m-10) cc_final: 0.8310 (m-10) REVERT: B 152 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.6676 (mt) REVERT: B 234 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.7604 (tp) REVERT: B 250 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9022 (mp) REVERT: B 404 LEU cc_start: 0.9300 (mt) cc_final: 0.9080 (mt) REVERT: B 441 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.5844 (mtpt) REVERT: B 465 LEU cc_start: 0.9105 (mt) cc_final: 0.8820 (mt) REVERT: B 480 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: B 491 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8383 (pp) REVERT: B 495 ARG cc_start: 0.9194 (tpt90) cc_final: 0.8823 (tpp80) REVERT: B 528 LEU cc_start: 0.9439 (mt) cc_final: 0.9229 (mt) REVERT: B 539 CYS cc_start: 0.7316 (t) cc_final: 0.6831 (t) REVERT: B 541 LEU cc_start: 0.8703 (mt) cc_final: 0.8366 (pp) REVERT: B 585 CYS cc_start: 0.6848 (t) cc_final: 0.5554 (t) REVERT: B 593 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.7619 (pp) REVERT: B 677 THR cc_start: 0.8107 (p) cc_final: 0.7557 (t) REVERT: B 699 ILE cc_start: 0.9275 (mt) cc_final: 0.8493 (mt) REVERT: B 719 CYS cc_start: 0.8812 (m) cc_final: 0.7953 (p) REVERT: B 803 MET cc_start: 0.8425 (ttp) cc_final: 0.8036 (tmm) REVERT: B 871 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6571 (pt) REVERT: B 907 ILE cc_start: 0.9195 (mp) cc_final: 0.8662 (mp) REVERT: B 915 ASP cc_start: 0.7069 (m-30) cc_final: 0.6786 (m-30) REVERT: B 937 PRO cc_start: 0.8316 (Cg_endo) cc_final: 0.7953 (Cg_exo) REVERT: B 962 MET cc_start: 0.8810 (ttt) cc_final: 0.8422 (tpp) REVERT: B 970 LYS cc_start: 0.9053 (ttpt) cc_final: 0.8744 (tppp) REVERT: B 985 ILE cc_start: 0.9358 (mm) cc_final: 0.9057 (mm) REVERT: B 1000 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8838 (mm) REVERT: B 1033 TYR cc_start: 0.8309 (m-80) cc_final: 0.8024 (t80) REVERT: B 1092 LEU cc_start: 0.8033 (mt) cc_final: 0.7711 (mt) REVERT: B 1093 LEU cc_start: 0.7111 (tp) cc_final: 0.6598 (tp) REVERT: B 1120 ILE cc_start: 0.5120 (OUTLIER) cc_final: 0.3615 (pp) REVERT: C 191 ILE cc_start: 0.9444 (mt) cc_final: 0.9046 (tp) REVERT: C 196 LEU cc_start: 0.9368 (mp) cc_final: 0.8981 (mm) REVERT: C 259 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7907 (t70) REVERT: C 321 LEU cc_start: 0.8641 (tp) cc_final: 0.8437 (tp) REVERT: E 18 THR cc_start: 0.8215 (m) cc_final: 0.7572 (p) REVERT: E 21 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8713 (mt-10) REVERT: E 35 VAL cc_start: 0.8909 (t) cc_final: 0.8652 (p) REVERT: E 50 MET cc_start: 0.7185 (mmm) cc_final: 0.6960 (mpp) REVERT: E 84 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: E 213 ILE cc_start: 0.7294 (tt) cc_final: 0.5999 (tt) REVERT: G 59 GLN cc_start: 0.8575 (tt0) cc_final: 0.8136 (tp-100) REVERT: H 22 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7479 (mtpp) REVERT: H 121 LEU cc_start: 0.9027 (mp) cc_final: 0.8814 (mp) REVERT: H 125 LEU cc_start: 0.8763 (mt) cc_final: 0.8555 (tp) REVERT: I 27 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7233 (t0) REVERT: I 95 ASN cc_start: 0.6418 (m110) cc_final: 0.5802 (p0) REVERT: J 5 VAL cc_start: 0.8364 (t) cc_final: 0.8066 (t) REVERT: J 48 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8789 (ttp80) REVERT: J 56 LEU cc_start: 0.9449 (mt) cc_final: 0.9194 (mt) REVERT: J 60 PHE cc_start: 0.8306 (m-80) cc_final: 0.8063 (m-80) REVERT: K 66 VAL cc_start: 0.8198 (m) cc_final: 0.7484 (p) REVERT: K 132 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: L 40 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8646 (tp) REVERT: M 28 LYS cc_start: 0.8346 (tptt) cc_final: 0.8009 (tppt) REVERT: M 38 PHE cc_start: 0.8521 (m-80) cc_final: 0.8205 (m-80) REVERT: M 62 TYR cc_start: 0.7986 (m-80) cc_final: 0.6385 (m-80) REVERT: M 66 THR cc_start: 0.7417 (p) cc_final: 0.6205 (p) REVERT: M 113 ILE cc_start: 0.8069 (mt) cc_final: 0.7863 (mm) REVERT: N 36 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8237 (tttt) REVERT: N 94 ASP cc_start: 0.1635 (OUTLIER) cc_final: 0.1333 (m-30) REVERT: N 131 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.3727 (mt) REVERT: O 149 LYS cc_start: 0.0897 (OUTLIER) cc_final: -0.3583 (pttp) REVERT: O 363 THR cc_start: 0.6519 (OUTLIER) cc_final: 0.6097 (t) REVERT: O 395 LEU cc_start: 0.3487 (OUTLIER) cc_final: 0.3140 (mt) REVERT: O 469 ARG cc_start: 0.0112 (mtm180) cc_final: -0.0239 (mtp180) REVERT: O 471 LYS cc_start: 0.6770 (ptpt) cc_final: 0.6408 (mttm) REVERT: O 543 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7198 (mp) REVERT: O 551 ARG cc_start: 0.2732 (ttp80) cc_final: 0.0637 (tpt170) REVERT: O 602 TYR cc_start: 0.4567 (OUTLIER) cc_final: 0.3828 (t80) outliers start: 362 outliers final: 68 residues processed: 1761 average time/residue: 0.6254 time to fit residues: 1737.0723 Evaluate side-chains 1021 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 924 time to evaluate : 4.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 472 optimal weight: 10.0000 chunk 424 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 286 optimal weight: 6.9990 chunk 226 optimal weight: 0.5980 chunk 438 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 508 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 76 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 431 GLN A 537 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN A 634 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN A 706 HIS A 730 GLN A 738 ASN A 798 HIS A 926 GLN ** A 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1113 HIS A1180 ASN A1314 GLN A1487 ASN A1503 HIS ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN A1633 GLN B 45 HIS ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 173 ASN B 212 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN B 361 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 823 GLN B 896 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B 975 HIS B 999 GLN B1008 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 ASN C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 335 GLN E 54 GLN E 113 GLN E 146 HIS ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 124 ASN I 125 ASN J 26 GLN J 64 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS K 106 GLN M 89 GLN N 50 GLN N 132 GLN N 170 HIS O 66 ASN O 173 HIS O 371 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 546 ASN O 547 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.824 44412 Z= 0.541 Angle : 0.781 22.531 60002 Z= 0.415 Chirality : 0.047 0.280 6174 Planarity : 0.005 0.078 7686 Dihedral : 14.313 88.375 7179 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.00 % Favored : 95.67 % Rotamer: Outliers : 0.24 % Allowed : 4.29 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 5522 helix: 1.06 (0.11), residues: 2210 sheet: -0.78 (0.17), residues: 753 loop : -1.21 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 143 HIS 0.018 0.002 HIS E 153 PHE 0.058 0.003 PHE B 440 TYR 0.042 0.003 TYR C 82 ARG 0.015 0.001 ARG K 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1069 time to evaluate : 4.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 ILE cc_start: 0.9139 (pt) cc_final: 0.8778 (mm) REVERT: A 597 LYS cc_start: 0.9187 (pttm) cc_final: 0.8972 (pttt) REVERT: A 675 SER cc_start: 0.9592 (m) cc_final: 0.9214 (p) REVERT: A 699 CYS cc_start: 0.7567 (p) cc_final: 0.7361 (p) REVERT: A 736 LEU cc_start: 0.9361 (mt) cc_final: 0.9067 (mt) REVERT: A 766 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7756 (mm-30) REVERT: A 771 PHE cc_start: 0.7579 (m-80) cc_final: 0.7374 (m-10) REVERT: A 793 ILE cc_start: 0.9182 (tp) cc_final: 0.8848 (tp) REVERT: A 952 LEU cc_start: 0.8268 (mm) cc_final: 0.7503 (mm) REVERT: A 995 TYR cc_start: 0.8764 (t80) cc_final: 0.8470 (t80) REVERT: A 1018 TYR cc_start: 0.7191 (t80) cc_final: 0.6519 (t80) REVERT: A 1144 LEU cc_start: 0.9360 (tp) cc_final: 0.9132 (pp) REVERT: A 1238 MET cc_start: 0.8231 (mtm) cc_final: 0.7773 (mtt) REVERT: A 1471 GLU cc_start: 0.7666 (tp30) cc_final: 0.7423 (tp30) REVERT: A 1479 ASP cc_start: 0.8516 (t70) cc_final: 0.8281 (t0) REVERT: A 1530 TRP cc_start: 0.9094 (m-10) cc_final: 0.8724 (m-10) REVERT: A 1566 ILE cc_start: 0.9231 (mt) cc_final: 0.9010 (mt) REVERT: A 1588 MET cc_start: 0.8334 (tpt) cc_final: 0.7953 (tpt) REVERT: A 1618 THR cc_start: 0.7256 (m) cc_final: 0.6905 (m) REVERT: B 235 GLN cc_start: 0.8254 (tt0) cc_final: 0.7995 (tt0) REVERT: B 409 TYR cc_start: 0.8543 (t80) cc_final: 0.8302 (t80) REVERT: B 461 MET cc_start: 0.8784 (tpp) cc_final: 0.7925 (mmt) REVERT: B 524 SER cc_start: 0.9304 (p) cc_final: 0.9067 (p) REVERT: B 528 LEU cc_start: 0.9536 (mt) cc_final: 0.9151 (mp) REVERT: B 535 ASP cc_start: 0.7964 (p0) cc_final: 0.7732 (p0) REVERT: B 641 TYR cc_start: 0.7809 (m-80) cc_final: 0.7426 (m-80) REVERT: B 677 THR cc_start: 0.8348 (p) cc_final: 0.7813 (t) REVERT: B 697 LEU cc_start: 0.8939 (mt) cc_final: 0.8695 (mp) REVERT: B 700 LEU cc_start: 0.9466 (mp) cc_final: 0.9259 (mp) REVERT: B 715 ASN cc_start: 0.9073 (m-40) cc_final: 0.8435 (m110) REVERT: B 719 CYS cc_start: 0.8807 (m) cc_final: 0.8569 (m) REVERT: B 726 MET cc_start: 0.8688 (ttp) cc_final: 0.8114 (ttp) REVERT: B 742 TYR cc_start: 0.8515 (m-10) cc_final: 0.6935 (m-10) REVERT: B 782 ASP cc_start: 0.8163 (p0) cc_final: 0.7359 (p0) REVERT: B 1039 MET cc_start: 0.2523 (tmm) cc_final: 0.1633 (tmm) REVERT: B 1074 MET cc_start: 0.8495 (mtt) cc_final: 0.8102 (mtp) REVERT: B 1184 TYR cc_start: 0.6369 (t80) cc_final: 0.5675 (t80) REVERT: C 188 ASP cc_start: 0.7484 (t0) cc_final: 0.7182 (t0) REVERT: C 191 ILE cc_start: 0.9337 (mt) cc_final: 0.9131 (mt) REVERT: C 192 LEU cc_start: 0.8851 (tp) cc_final: 0.8306 (tt) REVERT: C 229 LEU cc_start: 0.8217 (tp) cc_final: 0.8015 (tp) REVERT: C 255 VAL cc_start: 0.7518 (t) cc_final: 0.6830 (t) REVERT: D 25 THR cc_start: 0.7018 (p) cc_final: 0.6773 (p) REVERT: E 18 THR cc_start: 0.8332 (m) cc_final: 0.7636 (p) REVERT: E 112 TYR cc_start: 0.8067 (p90) cc_final: 0.7581 (p90) REVERT: E 213 ILE cc_start: 0.7730 (tt) cc_final: 0.6755 (tp) REVERT: F 118 LEU cc_start: 0.9343 (mt) cc_final: 0.8898 (mt) REVERT: G 172 ASP cc_start: 0.3972 (m-30) cc_final: 0.2937 (p0) REVERT: I 95 ASN cc_start: 0.6898 (m110) cc_final: 0.6510 (p0) REVERT: J 5 VAL cc_start: 0.8649 (t) cc_final: 0.8289 (t) REVERT: J 17 LYS cc_start: 0.9084 (mttp) cc_final: 0.8882 (mttm) REVERT: K 91 TYR cc_start: 0.7970 (p90) cc_final: 0.7726 (p90) REVERT: K 99 ASN cc_start: 0.8513 (m-40) cc_final: 0.8229 (m-40) REVERT: K 125 MET cc_start: 0.7838 (ptp) cc_final: 0.7039 (ptt) REVERT: K 135 PHE cc_start: 0.8351 (t80) cc_final: 0.8069 (t80) REVERT: K 138 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8217 (mmmt) REVERT: L 40 LEU cc_start: 0.8809 (tp) cc_final: 0.8568 (tt) REVERT: L 46 VAL cc_start: 0.7590 (t) cc_final: 0.7317 (m) REVERT: M 38 PHE cc_start: 0.8865 (m-80) cc_final: 0.8488 (m-80) REVERT: M 52 VAL cc_start: 0.8047 (t) cc_final: 0.7842 (t) REVERT: N 90 MET cc_start: 0.9012 (tpt) cc_final: 0.8619 (tpt) REVERT: N 145 ILE cc_start: 0.8765 (pt) cc_final: 0.8455 (mp) REVERT: O 378 THR cc_start: 0.2483 (m) cc_final: 0.2082 (m) REVERT: O 546 ASN cc_start: 0.8386 (m110) cc_final: 0.8067 (t0) outliers start: 10 outliers final: 1 residues processed: 1077 average time/residue: 0.5868 time to fit residues: 1002.7924 Evaluate side-chains 795 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 794 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 282 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 423 optimal weight: 0.9990 chunk 346 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 509 optimal weight: 30.0000 chunk 550 optimal weight: 20.0000 chunk 453 optimal weight: 20.0000 chunk 505 optimal weight: 40.0000 chunk 173 optimal weight: 7.9990 chunk 408 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN A 748 ASN A 753 ASN A 880 GLN A 887 ASN A 906 GLN ** A 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 HIS A1443 GLN A1564 ASN ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 323 ASN E 8 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS N 170 HIS ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 478 GLN O 533 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.949 44412 Z= 0.541 Angle : 0.742 18.643 60002 Z= 0.398 Chirality : 0.045 0.266 6174 Planarity : 0.005 0.114 7686 Dihedral : 14.376 85.075 7179 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.55 % Favored : 95.24 % Rotamer: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 5522 helix: 1.31 (0.11), residues: 2218 sheet: -0.56 (0.17), residues: 780 loop : -0.96 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP G 125 HIS 0.013 0.002 HIS A 221 PHE 0.061 0.003 PHE O 189 TYR 0.056 0.003 TYR C 82 ARG 0.017 0.001 ARG G 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 957 time to evaluate : 4.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.9387 (pttm) cc_final: 0.8268 (pttt) REVERT: A 658 LEU cc_start: 0.9359 (mt) cc_final: 0.9124 (mt) REVERT: A 675 SER cc_start: 0.9582 (m) cc_final: 0.9098 (p) REVERT: A 686 PHE cc_start: 0.8325 (m-80) cc_final: 0.8110 (m-80) REVERT: A 695 TYR cc_start: 0.9225 (m-10) cc_final: 0.9016 (m-80) REVERT: A 699 CYS cc_start: 0.7850 (p) cc_final: 0.7528 (p) REVERT: A 736 LEU cc_start: 0.9389 (mt) cc_final: 0.9174 (mt) REVERT: A 755 ILE cc_start: 0.8527 (mt) cc_final: 0.8280 (mt) REVERT: A 760 TRP cc_start: 0.8246 (m100) cc_final: 0.8004 (m100) REVERT: A 780 ILE cc_start: 0.9218 (pt) cc_final: 0.8854 (pt) REVERT: A 793 ILE cc_start: 0.9317 (tp) cc_final: 0.8912 (tp) REVERT: A 822 THR cc_start: 0.9397 (m) cc_final: 0.9161 (p) REVERT: A 833 LEU cc_start: 0.9134 (mp) cc_final: 0.8841 (mp) REVERT: A 934 LYS cc_start: 0.8822 (tptm) cc_final: 0.8254 (mmmm) REVERT: A 995 TYR cc_start: 0.8870 (t80) cc_final: 0.8627 (t80) REVERT: A 1018 TYR cc_start: 0.7234 (t80) cc_final: 0.6686 (t80) REVERT: A 1121 ASP cc_start: 0.7994 (p0) cc_final: 0.7394 (p0) REVERT: A 1190 SER cc_start: 0.9601 (p) cc_final: 0.9159 (t) REVERT: A 1238 MET cc_start: 0.8364 (mtm) cc_final: 0.7942 (mtt) REVERT: A 1471 GLU cc_start: 0.7885 (tp30) cc_final: 0.7510 (tp30) REVERT: A 1519 LEU cc_start: 0.8295 (mt) cc_final: 0.8091 (mt) REVERT: A 1530 TRP cc_start: 0.9238 (m-10) cc_final: 0.8727 (m-10) REVERT: A 1545 ASP cc_start: 0.7708 (t0) cc_final: 0.7499 (t0) REVERT: A 1618 THR cc_start: 0.7487 (m) cc_final: 0.7158 (m) REVERT: A 1647 ASN cc_start: 0.8542 (t0) cc_final: 0.7847 (t0) REVERT: A 1649 VAL cc_start: 0.8915 (t) cc_final: 0.8346 (t) REVERT: B 21 ARG cc_start: 0.8049 (tpt170) cc_final: 0.6905 (tpt170) REVERT: B 25 PHE cc_start: 0.8840 (m-10) cc_final: 0.8333 (m-80) REVERT: B 165 LEU cc_start: 0.9165 (mp) cc_final: 0.8912 (mp) REVERT: B 175 MET cc_start: 0.9130 (tpp) cc_final: 0.8058 (tpp) REVERT: B 215 MET cc_start: 0.8440 (mmm) cc_final: 0.7569 (mmm) REVERT: B 398 GLN cc_start: 0.9093 (pt0) cc_final: 0.8627 (pt0) REVERT: B 411 MET cc_start: 0.8811 (mmp) cc_final: 0.8505 (mmm) REVERT: B 415 GLU cc_start: 0.8521 (tp30) cc_final: 0.8197 (tp30) REVERT: B 528 LEU cc_start: 0.9695 (mt) cc_final: 0.9319 (mp) REVERT: B 641 TYR cc_start: 0.8120 (m-80) cc_final: 0.7641 (m-80) REVERT: B 659 ASP cc_start: 0.8928 (m-30) cc_final: 0.8506 (p0) REVERT: B 715 ASN cc_start: 0.9260 (m-40) cc_final: 0.8898 (m110) REVERT: B 717 TYR cc_start: 0.8184 (t80) cc_final: 0.7917 (t80) REVERT: B 723 LYS cc_start: 0.9426 (mtmt) cc_final: 0.9219 (mttt) REVERT: B 726 MET cc_start: 0.8907 (ttp) cc_final: 0.8352 (ttp) REVERT: B 741 LEU cc_start: 0.8833 (mt) cc_final: 0.8620 (mt) REVERT: B 742 TYR cc_start: 0.8226 (m-10) cc_final: 0.7887 (m-10) REVERT: B 745 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8739 (mm-40) REVERT: B 779 THR cc_start: 0.9159 (p) cc_final: 0.8851 (p) REVERT: B 782 ASP cc_start: 0.8898 (p0) cc_final: 0.7577 (p0) REVERT: B 904 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8840 (ttmm) REVERT: B 915 ASP cc_start: 0.7971 (m-30) cc_final: 0.7282 (m-30) REVERT: B 931 TRP cc_start: 0.9063 (t-100) cc_final: 0.8416 (t-100) REVERT: B 959 THR cc_start: 0.8554 (p) cc_final: 0.8020 (p) REVERT: B 970 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9168 (mmmm) REVERT: B 1000 LEU cc_start: 0.9186 (mm) cc_final: 0.8981 (mm) REVERT: B 1039 MET cc_start: 0.4102 (tmm) cc_final: 0.3540 (tmm) REVERT: C 63 ILE cc_start: 0.8687 (mp) cc_final: 0.8204 (mp) REVERT: C 188 ASP cc_start: 0.7906 (t0) cc_final: 0.7402 (t0) REVERT: C 191 ILE cc_start: 0.9381 (mt) cc_final: 0.9119 (mm) REVERT: C 207 HIS cc_start: 0.8527 (m90) cc_final: 0.8270 (m90) REVERT: D 94 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8441 (ttp80) REVERT: E 50 MET cc_start: 0.7431 (mpp) cc_final: 0.7222 (mpp) REVERT: E 112 TYR cc_start: 0.8781 (p90) cc_final: 0.8039 (p90) REVERT: E 213 ILE cc_start: 0.8184 (tt) cc_final: 0.7124 (tp) REVERT: F 85 MET cc_start: 0.6649 (ppp) cc_final: 0.5961 (ppp) REVERT: F 89 GLU cc_start: 0.8484 (pm20) cc_final: 0.8217 (mp0) REVERT: F 118 LEU cc_start: 0.9264 (mt) cc_final: 0.8763 (mt) REVERT: G 172 ASP cc_start: 0.4223 (m-30) cc_final: 0.3101 (p0) REVERT: I 70 SER cc_start: 0.4938 (p) cc_final: 0.4197 (p) REVERT: I 95 ASN cc_start: 0.6728 (m110) cc_final: 0.6480 (p0) REVERT: J 5 VAL cc_start: 0.9053 (t) cc_final: 0.8662 (t) REVERT: J 16 ASP cc_start: 0.8350 (p0) cc_final: 0.7741 (p0) REVERT: K 50 LEU cc_start: 0.8284 (mp) cc_final: 0.7794 (tt) REVERT: K 66 VAL cc_start: 0.8266 (m) cc_final: 0.7498 (p) REVERT: K 125 MET cc_start: 0.7956 (ptp) cc_final: 0.7185 (ptt) REVERT: M 97 VAL cc_start: 0.9094 (t) cc_final: 0.8782 (m) REVERT: N 90 MET cc_start: 0.8988 (tpt) cc_final: 0.8744 (tpt) REVERT: O 51 MET cc_start: 0.4070 (mtp) cc_final: 0.3868 (mtp) REVERT: O 546 ASN cc_start: 0.8464 (m110) cc_final: 0.8122 (t0) outliers start: 5 outliers final: 2 residues processed: 960 average time/residue: 0.5857 time to fit residues: 899.0255 Evaluate side-chains 726 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 724 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 503 optimal weight: 50.0000 chunk 383 optimal weight: 5.9990 chunk 264 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 342 optimal weight: 20.0000 chunk 511 optimal weight: 30.0000 chunk 541 optimal weight: 40.0000 chunk 267 optimal weight: 2.9990 chunk 484 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1151 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 399 HIS ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN B1165 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN O 94 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.942 44412 Z= 0.606 Angle : 0.831 18.503 60002 Z= 0.444 Chirality : 0.048 0.421 6174 Planarity : 0.006 0.081 7686 Dihedral : 14.826 168.096 7179 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 30.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.18 % Favored : 94.62 % Rotamer: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 5522 helix: 0.90 (0.11), residues: 2246 sheet: -0.47 (0.18), residues: 782 loop : -1.16 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.004 TRP B 143 HIS 0.013 0.003 HIS A 224 PHE 0.043 0.003 PHE E 96 TYR 0.038 0.003 TYR C 82 ARG 0.064 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 880 time to evaluate : 5.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LYS cc_start: 0.8851 (pttm) cc_final: 0.8430 (pttt) REVERT: A 633 MET cc_start: 0.7764 (mmm) cc_final: 0.7559 (mmm) REVERT: A 658 LEU cc_start: 0.9369 (mt) cc_final: 0.9110 (mt) REVERT: A 675 SER cc_start: 0.9645 (m) cc_final: 0.9364 (p) REVERT: A 695 TYR cc_start: 0.9217 (m-10) cc_final: 0.8985 (m-80) REVERT: A 699 CYS cc_start: 0.8038 (p) cc_final: 0.7777 (p) REVERT: A 755 ILE cc_start: 0.9234 (mt) cc_final: 0.8926 (mt) REVERT: A 760 TRP cc_start: 0.8557 (m100) cc_final: 0.8089 (m100) REVERT: A 780 ILE cc_start: 0.9293 (pt) cc_final: 0.9014 (pt) REVERT: A 782 ASP cc_start: 0.8312 (m-30) cc_final: 0.8074 (m-30) REVERT: A 816 LEU cc_start: 0.9348 (tp) cc_final: 0.9123 (tp) REVERT: A 830 MET cc_start: 0.8578 (mmp) cc_final: 0.8306 (mmm) REVERT: A 952 LEU cc_start: 0.8526 (mm) cc_final: 0.8189 (mm) REVERT: A 1018 TYR cc_start: 0.7507 (t80) cc_final: 0.6985 (t80) REVERT: A 1121 ASP cc_start: 0.7722 (p0) cc_final: 0.7038 (p0) REVERT: A 1170 MET cc_start: 0.8604 (mmm) cc_final: 0.8361 (mmt) REVERT: A 1187 ILE cc_start: 0.9040 (tp) cc_final: 0.8833 (tp) REVERT: A 1306 TYR cc_start: 0.6792 (m-80) cc_final: 0.6391 (m-80) REVERT: A 1471 GLU cc_start: 0.7927 (tp30) cc_final: 0.7475 (tp30) REVERT: A 1545 ASP cc_start: 0.8174 (t0) cc_final: 0.7927 (t0) REVERT: A 1618 THR cc_start: 0.7642 (m) cc_final: 0.7212 (m) REVERT: A 1649 VAL cc_start: 0.9091 (t) cc_final: 0.8819 (t) REVERT: B 21 ARG cc_start: 0.8209 (tpt170) cc_final: 0.7631 (tpt170) REVERT: B 25 PHE cc_start: 0.8847 (m-10) cc_final: 0.8431 (m-10) REVERT: B 215 MET cc_start: 0.8718 (mmm) cc_final: 0.8435 (mmm) REVERT: B 411 MET cc_start: 0.8960 (mmp) cc_final: 0.8650 (mmp) REVERT: B 495 ARG cc_start: 0.9605 (ttt-90) cc_final: 0.8990 (ttp80) REVERT: B 500 PHE cc_start: 0.9291 (m-80) cc_final: 0.9089 (m-80) REVERT: B 528 LEU cc_start: 0.9752 (mt) cc_final: 0.9491 (mp) REVERT: B 742 TYR cc_start: 0.8223 (m-10) cc_final: 0.7969 (m-10) REVERT: B 762 MET cc_start: 0.9030 (mmp) cc_final: 0.8816 (mmp) REVERT: B 782 ASP cc_start: 0.9116 (p0) cc_final: 0.8543 (p0) REVERT: B 904 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8744 (ttmm) REVERT: B 915 ASP cc_start: 0.7855 (m-30) cc_final: 0.7193 (m-30) REVERT: B 1005 TYR cc_start: 0.7763 (m-10) cc_final: 0.7459 (m-10) REVERT: B 1010 ASN cc_start: 0.9014 (m110) cc_final: 0.8781 (m110) REVERT: B 1013 MET cc_start: 0.8806 (tpt) cc_final: 0.8449 (mmm) REVERT: B 1039 MET cc_start: 0.6318 (tmm) cc_final: 0.5657 (tmm) REVERT: C 82 TYR cc_start: 0.8260 (m-80) cc_final: 0.7837 (m-10) REVERT: C 229 LEU cc_start: 0.8576 (tp) cc_final: 0.8240 (tp) REVERT: D 94 ARG cc_start: 0.9067 (ptt-90) cc_final: 0.8795 (ttp80) REVERT: E 50 MET cc_start: 0.7735 (mpp) cc_final: 0.7462 (mpp) REVERT: E 82 PHE cc_start: 0.8474 (m-80) cc_final: 0.8173 (m-80) REVERT: E 112 TYR cc_start: 0.8611 (p90) cc_final: 0.8146 (p90) REVERT: E 213 ILE cc_start: 0.8418 (tt) cc_final: 0.7284 (tp) REVERT: F 85 MET cc_start: 0.4410 (ppp) cc_final: 0.4182 (ppp) REVERT: F 118 LEU cc_start: 0.9294 (mt) cc_final: 0.8933 (mt) REVERT: G 170 HIS cc_start: 0.7863 (p-80) cc_final: 0.7519 (p-80) REVERT: J 5 VAL cc_start: 0.9196 (t) cc_final: 0.8747 (t) REVERT: J 16 ASP cc_start: 0.8519 (p0) cc_final: 0.8056 (p0) REVERT: J 41 LEU cc_start: 0.8282 (mp) cc_final: 0.7941 (mp) REVERT: J 58 GLU cc_start: 0.9425 (mm-30) cc_final: 0.8632 (tm-30) REVERT: K 69 ASP cc_start: 0.7336 (p0) cc_final: 0.7097 (p0) REVERT: K 124 LEU cc_start: 0.9365 (mt) cc_final: 0.9159 (mp) REVERT: K 125 MET cc_start: 0.8804 (ptp) cc_final: 0.8129 (ptt) REVERT: K 135 PHE cc_start: 0.8452 (t80) cc_final: 0.7849 (t80) REVERT: L 29 TYR cc_start: 0.8137 (m-10) cc_final: 0.7879 (m-10) REVERT: L 33 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8763 (tm-30) REVERT: M 52 VAL cc_start: 0.8125 (t) cc_final: 0.7917 (t) REVERT: O 508 ARG cc_start: 0.6357 (ptp-170) cc_final: 0.4634 (tmt-80) REVERT: O 525 MET cc_start: -0.1482 (tpt) cc_final: -0.1827 (tpt) outliers start: 4 outliers final: 1 residues processed: 883 average time/residue: 0.5780 time to fit residues: 820.6626 Evaluate side-chains 675 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 674 time to evaluate : 4.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 450 optimal weight: 6.9990 chunk 307 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 403 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 461 optimal weight: 40.0000 chunk 374 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 485 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN A 560 GLN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN B1008 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 207 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS N 44 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 moved from start: 0.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.941 44412 Z= 0.490 Angle : 0.663 19.110 60002 Z= 0.352 Chirality : 0.044 0.258 6174 Planarity : 0.004 0.058 7686 Dihedral : 14.626 174.505 7179 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.20 % Rotamer: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % 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: 0.07 (0.11), residues: 5522 helix: 1.33 (0.11), residues: 2243 sheet: -0.46 (0.18), residues: 781 loop : -0.94 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP B 143 HIS 0.008 0.002 HIS A 596 PHE 0.036 0.002 PHE A1535 TYR 0.042 0.002 TYR B 717 ARG 0.012 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 882 time to evaluate : 4.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASN cc_start: 0.8932 (m-40) cc_final: 0.8706 (m110) REVERT: A 628 PHE cc_start: 0.8139 (m-10) cc_final: 0.7845 (m-10) REVERT: A 658 LEU cc_start: 0.9231 (mt) cc_final: 0.8919 (mt) REVERT: A 671 GLN cc_start: 0.8464 (mt0) cc_final: 0.7635 (mt0) REVERT: A 675 SER cc_start: 0.9582 (m) cc_final: 0.9267 (p) REVERT: A 695 TYR cc_start: 0.9122 (m-10) cc_final: 0.8815 (m-80) REVERT: A 699 CYS cc_start: 0.7920 (p) cc_final: 0.7452 (p) REVERT: A 755 ILE cc_start: 0.9097 (mt) cc_final: 0.8768 (mt) REVERT: A 760 TRP cc_start: 0.8705 (m100) cc_final: 0.8230 (m100) REVERT: A 780 ILE cc_start: 0.9180 (pt) cc_final: 0.8874 (pt) REVERT: A 830 MET cc_start: 0.8497 (mmp) cc_final: 0.7951 (mmm) REVERT: A 833 LEU cc_start: 0.9466 (mp) cc_final: 0.9232 (mp) REVERT: A 907 VAL cc_start: 0.9137 (t) cc_final: 0.8657 (t) REVERT: A 995 TYR cc_start: 0.8899 (t80) cc_final: 0.8580 (t80) REVERT: A 1018 TYR cc_start: 0.7422 (t80) cc_final: 0.6859 (t80) REVERT: A 1021 ARG cc_start: 0.8865 (mmt180) cc_final: 0.7840 (mmt180) REVERT: A 1045 LEU cc_start: 0.8597 (tt) cc_final: 0.8323 (tp) REVERT: A 1121 ASP cc_start: 0.7989 (p0) cc_final: 0.7317 (p0) REVERT: A 1187 ILE cc_start: 0.9122 (tp) cc_final: 0.8880 (tp) REVERT: A 1200 MET cc_start: 0.8207 (mmp) cc_final: 0.7708 (mmp) REVERT: A 1306 TYR cc_start: 0.6475 (m-80) cc_final: 0.6180 (m-80) REVERT: B 21 ARG cc_start: 0.8111 (tpt170) cc_final: 0.7210 (tpt170) REVERT: B 25 PHE cc_start: 0.8714 (m-10) cc_final: 0.8484 (m-10) REVERT: B 215 MET cc_start: 0.8708 (mmm) cc_final: 0.8121 (mmm) REVERT: B 327 LEU cc_start: 0.9273 (mt) cc_final: 0.8936 (tp) REVERT: B 392 ASP cc_start: 0.8268 (m-30) cc_final: 0.8035 (m-30) REVERT: B 411 MET cc_start: 0.8826 (mmp) cc_final: 0.8411 (mmp) REVERT: B 415 GLU cc_start: 0.8553 (tp30) cc_final: 0.8117 (tp30) REVERT: B 495 ARG cc_start: 0.9557 (ttt-90) cc_final: 0.8949 (ttp80) REVERT: B 500 PHE cc_start: 0.9219 (m-80) cc_final: 0.9001 (m-80) REVERT: B 528 LEU cc_start: 0.9683 (mt) cc_final: 0.9432 (mp) REVERT: B 542 LEU cc_start: 0.8913 (tp) cc_final: 0.8699 (tp) REVERT: B 592 ILE cc_start: 0.8773 (tt) cc_final: 0.8508 (tt) REVERT: B 641 TYR cc_start: 0.7982 (m-80) cc_final: 0.7676 (m-80) REVERT: B 715 ASN cc_start: 0.9152 (m-40) cc_final: 0.8719 (m110) REVERT: B 742 TYR cc_start: 0.8143 (m-10) cc_final: 0.7868 (m-10) REVERT: B 763 ASP cc_start: 0.8202 (t0) cc_final: 0.7768 (t0) REVERT: B 782 ASP cc_start: 0.8992 (p0) cc_final: 0.8463 (p0) REVERT: B 915 ASP cc_start: 0.7754 (m-30) cc_final: 0.7157 (m-30) REVERT: B 931 TRP cc_start: 0.8579 (t-100) cc_final: 0.8076 (t-100) REVERT: B 935 ASP cc_start: 0.8144 (t0) cc_final: 0.7112 (t0) REVERT: B 1005 TYR cc_start: 0.7466 (m-10) cc_final: 0.7256 (m-10) REVERT: B 1010 ASN cc_start: 0.9073 (m110) cc_final: 0.8862 (m110) REVERT: B 1013 MET cc_start: 0.8758 (tpt) cc_final: 0.8423 (mmm) REVERT: B 1039 MET cc_start: 0.6844 (tmm) cc_final: 0.6055 (tmm) REVERT: B 1084 THR cc_start: 0.8476 (p) cc_final: 0.8251 (p) REVERT: C 82 TYR cc_start: 0.8144 (m-80) cc_final: 0.7870 (m-10) REVERT: D 94 ARG cc_start: 0.9163 (ptt-90) cc_final: 0.8611 (ttp80) REVERT: E 7 ARG cc_start: 0.8548 (tpt170) cc_final: 0.8275 (tpt170) REVERT: E 22 MET cc_start: 0.8507 (tpt) cc_final: 0.8250 (tpt) REVERT: E 50 MET cc_start: 0.7849 (mpp) cc_final: 0.7579 (mpp) REVERT: E 75 MET cc_start: 0.4366 (ptt) cc_final: 0.3946 (ptt) REVERT: E 82 PHE cc_start: 0.8411 (m-80) cc_final: 0.8060 (m-80) REVERT: E 213 ILE cc_start: 0.8279 (tt) cc_final: 0.7213 (tp) REVERT: G 85 GLU cc_start: 0.5791 (pm20) cc_final: 0.5160 (pm20) REVERT: G 170 HIS cc_start: 0.7800 (p-80) cc_final: 0.7559 (p-80) REVERT: H 22 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8028 (ttpt) REVERT: J 5 VAL cc_start: 0.9149 (t) cc_final: 0.8707 (t) REVERT: J 16 ASP cc_start: 0.8539 (p0) cc_final: 0.8135 (p0) REVERT: J 41 LEU cc_start: 0.8234 (mp) cc_final: 0.8031 (mp) REVERT: J 58 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8812 (tp30) REVERT: J 60 PHE cc_start: 0.8550 (m-80) cc_final: 0.8310 (m-10) REVERT: K 135 PHE cc_start: 0.8453 (t80) cc_final: 0.8059 (t80) REVERT: L 33 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8498 (tm-30) REVERT: M 52 VAL cc_start: 0.7814 (t) cc_final: 0.7530 (p) outliers start: 2 outliers final: 0 residues processed: 884 average time/residue: 0.5895 time to fit residues: 835.1384 Evaluate side-chains 682 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 682 time to evaluate : 5.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 182 optimal weight: 10.0000 chunk 487 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 317 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 541 optimal weight: 40.0000 chunk 449 optimal weight: 40.0000 chunk 250 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 179 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN B 896 GLN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN C 99 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 ASN O 546 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.7664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.939 44412 Z= 0.526 Angle : 0.703 18.645 60002 Z= 0.371 Chirality : 0.044 0.308 6174 Planarity : 0.005 0.130 7686 Dihedral : 14.536 176.136 7179 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.22 % Favored : 94.60 % Rotamer: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % 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: -0.02 (0.11), residues: 5522 helix: 1.26 (0.11), residues: 2266 sheet: -0.50 (0.18), residues: 768 loop : -1.04 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP B 143 HIS 0.010 0.002 HIS B 952 PHE 0.039 0.002 PHE N 29 TYR 0.052 0.002 TYR G 53 ARG 0.012 0.001 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 852 time to evaluate : 5.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7322 (m-80) cc_final: 0.6789 (m-80) REVERT: A 130 ILE cc_start: 0.8521 (mm) cc_final: 0.8154 (mp) REVERT: A 658 LEU cc_start: 0.9275 (mt) cc_final: 0.9049 (mt) REVERT: A 671 GLN cc_start: 0.8637 (mt0) cc_final: 0.8365 (mt0) REVERT: A 675 SER cc_start: 0.9592 (m) cc_final: 0.9266 (p) REVERT: A 695 TYR cc_start: 0.9256 (m-10) cc_final: 0.9043 (m-80) REVERT: A 780 ILE cc_start: 0.9251 (pt) cc_final: 0.8988 (pt) REVERT: A 782 ASP cc_start: 0.8315 (m-30) cc_final: 0.8109 (m-30) REVERT: A 830 MET cc_start: 0.8492 (mmp) cc_final: 0.7974 (mmm) REVERT: A 952 LEU cc_start: 0.8656 (mm) cc_final: 0.8431 (mm) REVERT: A 995 TYR cc_start: 0.8964 (t80) cc_final: 0.8662 (t80) REVERT: A 1121 ASP cc_start: 0.8149 (p0) cc_final: 0.7547 (p0) REVERT: A 1144 LEU cc_start: 0.9390 (tp) cc_final: 0.9095 (tt) REVERT: A 1306 TYR cc_start: 0.6566 (m-80) cc_final: 0.5977 (m-80) REVERT: A 1471 GLU cc_start: 0.7799 (tp30) cc_final: 0.7102 (tp30) REVERT: A 1519 LEU cc_start: 0.8044 (mm) cc_final: 0.7830 (mm) REVERT: B 25 PHE cc_start: 0.8716 (m-10) cc_final: 0.8359 (m-10) REVERT: B 215 MET cc_start: 0.8717 (mmm) cc_final: 0.8472 (mmm) REVERT: B 415 GLU cc_start: 0.8565 (tp30) cc_final: 0.8071 (tp30) REVERT: B 495 ARG cc_start: 0.9602 (ttt-90) cc_final: 0.8916 (ttp80) REVERT: B 500 PHE cc_start: 0.9246 (m-80) cc_final: 0.9027 (m-80) REVERT: B 504 HIS cc_start: 0.7983 (t70) cc_final: 0.7509 (t70) REVERT: B 528 LEU cc_start: 0.9691 (mt) cc_final: 0.9456 (mp) REVERT: B 542 LEU cc_start: 0.8902 (tp) cc_final: 0.8698 (tp) REVERT: B 715 ASN cc_start: 0.9140 (m-40) cc_final: 0.8756 (m-40) REVERT: B 717 TYR cc_start: 0.8278 (t80) cc_final: 0.7943 (t80) REVERT: B 742 TYR cc_start: 0.8218 (m-10) cc_final: 0.7903 (m-10) REVERT: B 763 ASP cc_start: 0.8241 (t0) cc_final: 0.7827 (t0) REVERT: B 782 ASP cc_start: 0.8968 (p0) cc_final: 0.8495 (p0) REVERT: B 785 ASP cc_start: 0.7251 (m-30) cc_final: 0.6871 (m-30) REVERT: B 915 ASP cc_start: 0.7816 (m-30) cc_final: 0.7091 (m-30) REVERT: B 1039 MET cc_start: 0.5848 (tmm) cc_final: 0.5368 (tmm) REVERT: C 82 TYR cc_start: 0.8248 (m-80) cc_final: 0.7871 (m-10) REVERT: D 94 ARG cc_start: 0.9161 (ptt-90) cc_final: 0.8552 (ttp80) REVERT: E 50 MET cc_start: 0.8029 (mpp) cc_final: 0.7754 (mpp) REVERT: E 75 MET cc_start: 0.5138 (ptt) cc_final: 0.4747 (ptt) REVERT: E 82 PHE cc_start: 0.8385 (m-80) cc_final: 0.8083 (m-80) REVERT: E 213 ILE cc_start: 0.8373 (tt) cc_final: 0.7382 (tp) REVERT: F 90 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7691 (mmm-85) REVERT: F 118 LEU cc_start: 0.9326 (mt) cc_final: 0.9048 (mt) REVERT: I 70 SER cc_start: 0.5885 (p) cc_final: 0.5379 (p) REVERT: I 94 MET cc_start: -0.0106 (mmt) cc_final: -0.0456 (tpp) REVERT: J 16 ASP cc_start: 0.8538 (p0) cc_final: 0.7979 (p0) REVERT: J 41 LEU cc_start: 0.8520 (mp) cc_final: 0.8251 (mp) REVERT: J 58 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8600 (tm-30) REVERT: K 135 PHE cc_start: 0.8413 (t80) cc_final: 0.8098 (t80) REVERT: L 33 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8707 (tm-30) REVERT: M 51 PHE cc_start: 0.7320 (m-80) cc_final: 0.7112 (m-10) REVERT: N 27 ASP cc_start: 0.9430 (t0) cc_final: 0.8840 (t70) REVERT: O 156 MET cc_start: 0.6507 (mmt) cc_final: 0.6226 (mmt) REVERT: O 508 ARG cc_start: 0.5367 (ptp-170) cc_final: 0.4022 (tmt-80) outliers start: 2 outliers final: 1 residues processed: 853 average time/residue: 0.5752 time to fit residues: 790.5454 Evaluate side-chains 669 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 668 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 522 optimal weight: 50.0000 chunk 61 optimal weight: 0.9990 chunk 308 optimal weight: 2.9990 chunk 395 optimal weight: 0.9990 chunk 306 optimal weight: 8.9990 chunk 456 optimal weight: 20.0000 chunk 302 optimal weight: 10.0000 chunk 539 optimal weight: 9.9990 chunk 337 optimal weight: 1.9990 chunk 329 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN A1320 GLN ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS G 150 HIS O 451 ASN ** O 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.7889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.938 44412 Z= 0.493 Angle : 0.668 18.892 60002 Z= 0.351 Chirality : 0.044 0.265 6174 Planarity : 0.004 0.069 7686 Dihedral : 14.475 177.347 7179 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Rotamer: Outliers : 0.02 % Allowed : 1.63 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % 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: 0.07 (0.11), residues: 5522 helix: 1.39 (0.11), residues: 2260 sheet: -0.52 (0.18), residues: 762 loop : -1.01 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP G 166 HIS 0.010 0.001 HIS G 144 PHE 0.038 0.002 PHE N 29 TYR 0.039 0.002 TYR G 53 ARG 0.010 0.001 ARG B1076 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 853 time to evaluate : 4.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7339 (m-80) cc_final: 0.6841 (m-80) REVERT: A 125 LEU cc_start: 0.8897 (mt) cc_final: 0.7384 (mt) REVERT: A 130 ILE cc_start: 0.8434 (mm) cc_final: 0.7914 (mp) REVERT: A 658 LEU cc_start: 0.9215 (mt) cc_final: 0.8886 (mt) REVERT: A 671 GLN cc_start: 0.8567 (mt0) cc_final: 0.8143 (mt0) REVERT: A 675 SER cc_start: 0.9533 (m) cc_final: 0.9251 (p) REVERT: A 695 TYR cc_start: 0.9225 (m-10) cc_final: 0.9016 (m-80) REVERT: A 726 TRP cc_start: 0.8488 (m-90) cc_final: 0.7297 (m-90) REVERT: A 760 TRP cc_start: 0.8830 (m100) cc_final: 0.8178 (m100) REVERT: A 780 ILE cc_start: 0.9161 (pt) cc_final: 0.8926 (pt) REVERT: A 830 MET cc_start: 0.8537 (mmp) cc_final: 0.8098 (mmp) REVERT: A 995 TYR cc_start: 0.8884 (t80) cc_final: 0.8583 (t80) REVERT: A 1018 TYR cc_start: 0.7064 (t80) cc_final: 0.6749 (t80) REVERT: A 1021 ARG cc_start: 0.8781 (mmt180) cc_final: 0.8040 (mmt180) REVERT: A 1121 ASP cc_start: 0.8161 (p0) cc_final: 0.7545 (p0) REVERT: A 1144 LEU cc_start: 0.9319 (tp) cc_final: 0.9016 (tt) REVERT: A 1200 MET cc_start: 0.8766 (mmp) cc_final: 0.8115 (mmp) REVERT: A 1306 TYR cc_start: 0.6640 (m-80) cc_final: 0.6281 (m-80) REVERT: A 1519 LEU cc_start: 0.7792 (mm) cc_final: 0.7513 (mm) REVERT: B 25 PHE cc_start: 0.8658 (m-10) cc_final: 0.8328 (m-10) REVERT: B 200 GLU cc_start: 0.8682 (mt-10) cc_final: 0.7907 (mt-10) REVERT: B 215 MET cc_start: 0.8710 (mmm) cc_final: 0.8399 (mmm) REVERT: B 277 LEU cc_start: 0.9238 (mt) cc_final: 0.8973 (mt) REVERT: B 411 MET cc_start: 0.8829 (mmp) cc_final: 0.8204 (mmm) REVERT: B 414 LYS cc_start: 0.8775 (ptpp) cc_final: 0.8530 (pttt) REVERT: B 415 GLU cc_start: 0.8542 (tp30) cc_final: 0.8251 (tp30) REVERT: B 495 ARG cc_start: 0.9496 (ttt-90) cc_final: 0.8946 (ttp80) REVERT: B 500 PHE cc_start: 0.9194 (m-80) cc_final: 0.8972 (m-80) REVERT: B 528 LEU cc_start: 0.9682 (mt) cc_final: 0.9447 (mp) REVERT: B 542 LEU cc_start: 0.8856 (tp) cc_final: 0.8650 (tp) REVERT: B 591 LYS cc_start: 0.9177 (tmtt) cc_final: 0.8831 (tptt) REVERT: B 592 ILE cc_start: 0.8492 (tt) cc_final: 0.7695 (tt) REVERT: B 715 ASN cc_start: 0.9102 (m-40) cc_final: 0.8646 (m110) REVERT: B 717 TYR cc_start: 0.8212 (t80) cc_final: 0.7493 (t80) REVERT: B 734 CYS cc_start: 0.8123 (p) cc_final: 0.7896 (p) REVERT: B 742 TYR cc_start: 0.8234 (m-10) cc_final: 0.7673 (m-10) REVERT: B 762 MET cc_start: 0.9242 (mmp) cc_final: 0.8844 (mmp) REVERT: B 763 ASP cc_start: 0.8243 (t0) cc_final: 0.7814 (t0) REVERT: B 782 ASP cc_start: 0.9044 (p0) cc_final: 0.8543 (p0) REVERT: B 785 ASP cc_start: 0.7241 (m-30) cc_final: 0.6762 (m-30) REVERT: B 886 ASN cc_start: 0.8344 (m-40) cc_final: 0.8047 (m110) REVERT: B 931 TRP cc_start: 0.8735 (t-100) cc_final: 0.8071 (t-100) REVERT: B 935 ASP cc_start: 0.8432 (t0) cc_final: 0.7457 (t0) REVERT: B 1013 MET cc_start: 0.8799 (tpt) cc_final: 0.8570 (tpp) REVERT: B 1039 MET cc_start: 0.6141 (tmm) cc_final: 0.5637 (tmm) REVERT: B 1192 MET cc_start: 0.5954 (mmp) cc_final: 0.5487 (mmm) REVERT: C 82 TYR cc_start: 0.8208 (m-80) cc_final: 0.7725 (m-10) REVERT: D 94 ARG cc_start: 0.9150 (ptt-90) cc_final: 0.8301 (ttp80) REVERT: E 50 MET cc_start: 0.8147 (mpp) cc_final: 0.7792 (mpp) REVERT: E 75 MET cc_start: 0.5219 (ptt) cc_final: 0.4897 (ptt) REVERT: E 82 PHE cc_start: 0.8341 (m-80) cc_final: 0.8048 (m-80) REVERT: E 213 ILE cc_start: 0.8435 (tt) cc_final: 0.7448 (tp) REVERT: I 70 SER cc_start: 0.5855 (p) cc_final: 0.5415 (p) REVERT: J 16 ASP cc_start: 0.8396 (p0) cc_final: 0.7835 (p0) REVERT: J 41 LEU cc_start: 0.8556 (mp) cc_final: 0.8220 (mp) REVERT: J 58 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8511 (tm-30) REVERT: J 60 PHE cc_start: 0.8653 (m-10) cc_final: 0.8423 (m-10) REVERT: K 124 LEU cc_start: 0.9268 (mm) cc_final: 0.8981 (mm) REVERT: K 135 PHE cc_start: 0.8350 (t80) cc_final: 0.8098 (t80) REVERT: L 33 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8670 (tm-30) REVERT: M 23 VAL cc_start: 0.7105 (m) cc_final: 0.6897 (p) REVERT: M 38 PHE cc_start: 0.8908 (m-80) cc_final: 0.8681 (m-80) REVERT: N 27 ASP cc_start: 0.9411 (t0) cc_final: 0.8781 (t70) REVERT: N 110 LEU cc_start: 0.9692 (mt) cc_final: 0.9439 (mt) outliers start: 1 outliers final: 0 residues processed: 854 average time/residue: 0.5641 time to fit residues: 777.1749 Evaluate side-chains 671 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 333 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 322 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 343 optimal weight: 6.9990 chunk 367 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 424 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.8164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.938 44412 Z= 0.485 Angle : 0.665 18.831 60002 Z= 0.347 Chirality : 0.045 0.283 6174 Planarity : 0.004 0.065 7686 Dihedral : 14.348 177.052 7179 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.09 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % 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: 0.18 (0.11), residues: 5522 helix: 1.51 (0.11), residues: 2242 sheet: -0.48 (0.19), residues: 731 loop : -0.96 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 166 HIS 0.009 0.001 HIS G 20 PHE 0.036 0.002 PHE J 60 TYR 0.038 0.002 TYR G 53 ARG 0.007 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 849 time to evaluate : 4.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7281 (m-80) cc_final: 0.6826 (m-80) REVERT: A 671 GLN cc_start: 0.8591 (mt0) cc_final: 0.8110 (mt0) REVERT: A 675 SER cc_start: 0.9548 (m) cc_final: 0.9297 (p) REVERT: A 726 TRP cc_start: 0.8464 (m-90) cc_final: 0.7292 (m-90) REVERT: A 780 ILE cc_start: 0.9158 (pt) cc_final: 0.8916 (pt) REVERT: A 830 MET cc_start: 0.8424 (mmp) cc_final: 0.7783 (mmp) REVERT: A 995 TYR cc_start: 0.8884 (t80) cc_final: 0.8550 (t80) REVERT: A 1121 ASP cc_start: 0.8166 (p0) cc_final: 0.7551 (p0) REVERT: A 1306 TYR cc_start: 0.6650 (m-80) cc_final: 0.6359 (m-80) REVERT: A 1479 ASP cc_start: 0.8715 (m-30) cc_final: 0.8491 (t0) REVERT: A 1519 LEU cc_start: 0.7757 (mm) cc_final: 0.7520 (mm) REVERT: A 1524 VAL cc_start: 0.8847 (m) cc_final: 0.8537 (m) REVERT: B 21 ARG cc_start: 0.7729 (tpt170) cc_final: 0.7099 (tpt170) REVERT: B 25 PHE cc_start: 0.8594 (m-10) cc_final: 0.8083 (m-10) REVERT: B 200 GLU cc_start: 0.8713 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 215 MET cc_start: 0.8728 (mmm) cc_final: 0.8470 (mmm) REVERT: B 277 LEU cc_start: 0.9210 (mt) cc_final: 0.8956 (mt) REVERT: B 373 MET cc_start: 0.8960 (mmm) cc_final: 0.8607 (mmt) REVERT: B 377 MET cc_start: 0.8630 (mmm) cc_final: 0.8386 (mmm) REVERT: B 411 MET cc_start: 0.8899 (mmp) cc_final: 0.8285 (mmm) REVERT: B 414 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8518 (pttt) REVERT: B 415 GLU cc_start: 0.8429 (tp30) cc_final: 0.8179 (tp30) REVERT: B 495 ARG cc_start: 0.9516 (ttt-90) cc_final: 0.8940 (ttp80) REVERT: B 500 PHE cc_start: 0.9135 (m-80) cc_final: 0.8884 (m-80) REVERT: B 528 LEU cc_start: 0.9683 (mt) cc_final: 0.9424 (mp) REVERT: B 592 ILE cc_start: 0.8433 (tt) cc_final: 0.8197 (tt) REVERT: B 696 ILE cc_start: 0.9656 (pt) cc_final: 0.9142 (tt) REVERT: B 717 TYR cc_start: 0.8259 (t80) cc_final: 0.7515 (t80) REVERT: B 734 CYS cc_start: 0.8183 (p) cc_final: 0.7941 (p) REVERT: B 740 LYS cc_start: 0.9005 (tmmt) cc_final: 0.8217 (ttpp) REVERT: B 742 TYR cc_start: 0.8076 (m-10) cc_final: 0.7633 (m-10) REVERT: B 762 MET cc_start: 0.9319 (mmp) cc_final: 0.8947 (mmp) REVERT: B 763 ASP cc_start: 0.8223 (t0) cc_final: 0.7716 (t0) REVERT: B 782 ASP cc_start: 0.9006 (p0) cc_final: 0.8537 (p0) REVERT: B 785 ASP cc_start: 0.7146 (m-30) cc_final: 0.6618 (m-30) REVERT: B 1013 MET cc_start: 0.8907 (tpt) cc_final: 0.8677 (tpp) REVERT: B 1039 MET cc_start: 0.6506 (tmm) cc_final: 0.5872 (tmm) REVERT: C 82 TYR cc_start: 0.8219 (m-80) cc_final: 0.7583 (m-10) REVERT: C 192 LEU cc_start: 0.9291 (tp) cc_final: 0.8857 (mm) REVERT: D 37 LEU cc_start: 0.9101 (pp) cc_final: 0.8838 (mm) REVERT: D 94 ARG cc_start: 0.9100 (ptt-90) cc_final: 0.8501 (ttp80) REVERT: E 50 MET cc_start: 0.8261 (mpp) cc_final: 0.7953 (mpp) REVERT: E 75 MET cc_start: 0.5208 (ptt) cc_final: 0.4466 (ptt) REVERT: E 82 PHE cc_start: 0.8451 (m-80) cc_final: 0.8100 (m-80) REVERT: E 213 ILE cc_start: 0.8540 (tt) cc_final: 0.7909 (pt) REVERT: F 118 LEU cc_start: 0.9325 (mt) cc_final: 0.9105 (mt) REVERT: F 123 LYS cc_start: 0.8983 (pttt) cc_final: 0.8775 (pttm) REVERT: I 70 SER cc_start: 0.5937 (p) cc_final: 0.5489 (p) REVERT: I 94 MET cc_start: -0.0260 (mmt) cc_final: -0.0644 (tpp) REVERT: J 16 ASP cc_start: 0.8752 (p0) cc_final: 0.8468 (p0) REVERT: J 41 LEU cc_start: 0.8493 (mp) cc_final: 0.7956 (mp) REVERT: J 58 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8859 (tp30) REVERT: J 60 PHE cc_start: 0.8654 (m-10) cc_final: 0.8444 (m-10) REVERT: K 135 PHE cc_start: 0.8305 (t80) cc_final: 0.8089 (t80) REVERT: L 33 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8654 (tm-30) REVERT: M 23 VAL cc_start: 0.7226 (m) cc_final: 0.6994 (p) REVERT: N 27 ASP cc_start: 0.9395 (t0) cc_final: 0.8779 (t70) outliers start: 0 outliers final: 0 residues processed: 849 average time/residue: 0.5743 time to fit residues: 788.4177 Evaluate side-chains 666 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 4.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 490 optimal weight: 7.9990 chunk 517 optimal weight: 40.0000 chunk 471 optimal weight: 50.0000 chunk 502 optimal weight: 50.0000 chunk 516 optimal weight: 50.0000 chunk 302 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 394 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 454 optimal weight: 6.9990 chunk 475 optimal weight: 0.8980 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 HIS ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 ASN C 93 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.8688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.911 44412 Z= 0.540 Angle : 0.730 19.447 60002 Z= 0.387 Chirality : 0.045 0.331 6174 Planarity : 0.005 0.062 7686 Dihedral : 14.368 177.198 7179 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.74 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % 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: -0.03 (0.11), residues: 5522 helix: 1.34 (0.11), residues: 2247 sheet: -0.70 (0.18), residues: 768 loop : -1.04 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 143 HIS 0.013 0.002 HIS A 596 PHE 0.034 0.002 PHE B 440 TYR 0.037 0.002 TYR G 53 ARG 0.012 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 829 time to evaluate : 5.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7324 (m-80) cc_final: 0.6799 (m-80) REVERT: A 481 ARG cc_start: 0.7945 (tmm-80) cc_final: 0.7695 (ptm-80) REVERT: A 590 ASN cc_start: 0.8367 (m-40) cc_final: 0.8028 (m-40) REVERT: A 671 GLN cc_start: 0.8697 (mt0) cc_final: 0.8201 (mt0) REVERT: A 675 SER cc_start: 0.9531 (m) cc_final: 0.9295 (p) REVERT: A 695 TYR cc_start: 0.9050 (m-80) cc_final: 0.8526 (m-80) REVERT: A 726 TRP cc_start: 0.8722 (m-90) cc_final: 0.7202 (m-90) REVERT: A 830 MET cc_start: 0.8517 (mmp) cc_final: 0.7795 (mmp) REVERT: A 939 ASN cc_start: 0.9339 (m110) cc_final: 0.9092 (t0) REVERT: A 1121 ASP cc_start: 0.8245 (p0) cc_final: 0.7679 (p0) REVERT: A 1306 TYR cc_start: 0.6820 (m-80) cc_final: 0.6551 (m-80) REVERT: A 1471 GLU cc_start: 0.8245 (tp30) cc_final: 0.7739 (tp30) REVERT: B 21 ARG cc_start: 0.7733 (tpt170) cc_final: 0.7261 (tpt170) REVERT: B 25 PHE cc_start: 0.8569 (m-10) cc_final: 0.7960 (m-10) REVERT: B 215 MET cc_start: 0.8723 (mmm) cc_final: 0.8446 (mmm) REVERT: B 373 MET cc_start: 0.8995 (mmm) cc_final: 0.8621 (mmt) REVERT: B 415 GLU cc_start: 0.8620 (tp30) cc_final: 0.8312 (tp30) REVERT: B 495 ARG cc_start: 0.9544 (ttt-90) cc_final: 0.9028 (ttp80) REVERT: B 500 PHE cc_start: 0.9231 (m-80) cc_final: 0.8993 (m-80) REVERT: B 528 LEU cc_start: 0.9698 (mt) cc_final: 0.9456 (mp) REVERT: B 542 LEU cc_start: 0.8896 (tp) cc_final: 0.8661 (tp) REVERT: B 715 ASN cc_start: 0.9074 (m110) cc_final: 0.8827 (m110) REVERT: B 734 CYS cc_start: 0.8245 (p) cc_final: 0.7978 (p) REVERT: B 740 LYS cc_start: 0.9019 (tmmt) cc_final: 0.8174 (ttpp) REVERT: B 742 TYR cc_start: 0.8111 (m-10) cc_final: 0.7571 (m-10) REVERT: B 763 ASP cc_start: 0.8272 (t0) cc_final: 0.7725 (t0) REVERT: B 769 PHE cc_start: 0.8757 (p90) cc_final: 0.8539 (p90) REVERT: B 782 ASP cc_start: 0.8947 (p0) cc_final: 0.8496 (p0) REVERT: B 785 ASP cc_start: 0.7266 (m-30) cc_final: 0.6746 (m-30) REVERT: B 958 MET cc_start: 0.8821 (pmm) cc_final: 0.8409 (pmm) REVERT: B 1013 MET cc_start: 0.8899 (tpt) cc_final: 0.8608 (tpp) REVERT: B 1039 MET cc_start: 0.7448 (tmm) cc_final: 0.6690 (tmm) REVERT: B 1186 ASP cc_start: 0.7502 (t0) cc_final: 0.7129 (t0) REVERT: C 82 TYR cc_start: 0.8230 (m-10) cc_final: 0.7833 (m-10) REVERT: D 94 ARG cc_start: 0.9212 (ptt-90) cc_final: 0.8398 (ttp80) REVERT: E 50 MET cc_start: 0.8192 (mpp) cc_final: 0.7865 (mpp) REVERT: E 82 PHE cc_start: 0.8618 (m-80) cc_final: 0.8299 (m-80) REVERT: E 213 ILE cc_start: 0.8659 (tt) cc_final: 0.8116 (pt) REVERT: F 118 LEU cc_start: 0.9336 (mt) cc_final: 0.8893 (mt) REVERT: H 22 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7681 (tttt) REVERT: I 94 MET cc_start: -0.0124 (mmt) cc_final: -0.0535 (tpp) REVERT: J 16 ASP cc_start: 0.8580 (p0) cc_final: 0.8153 (p0) REVERT: J 60 PHE cc_start: 0.8756 (m-10) cc_final: 0.8551 (m-10) REVERT: K 135 PHE cc_start: 0.8371 (t80) cc_final: 0.8164 (t80) REVERT: L 33 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8805 (tm-30) REVERT: M 51 PHE cc_start: 0.7029 (m-80) cc_final: 0.6787 (m-10) REVERT: M 100 VAL cc_start: 0.8079 (t) cc_final: 0.7784 (t) REVERT: N 27 ASP cc_start: 0.9291 (t0) cc_final: 0.8739 (t70) REVERT: N 110 LEU cc_start: 0.9663 (mt) cc_final: 0.9334 (mt) REVERT: O 51 MET cc_start: 0.4030 (ttt) cc_final: 0.3675 (ttt) REVERT: O 156 MET cc_start: 0.6421 (mmt) cc_final: 0.6167 (mmt) REVERT: O 433 LYS cc_start: 0.5776 (pptt) cc_final: 0.4767 (pptt) outliers start: 0 outliers final: 0 residues processed: 829 average time/residue: 0.5794 time to fit residues: 779.6105 Evaluate side-chains 651 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 651 time to evaluate : 4.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 501 optimal weight: 40.0000 chunk 330 optimal weight: 30.0000 chunk 531 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 369 optimal weight: 0.9990 chunk 557 optimal weight: 20.0000 chunk 513 optimal weight: 40.0000 chunk 444 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.9255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.946 44412 Z= 0.582 Angle : 0.816 20.047 60002 Z= 0.432 Chirality : 0.047 0.437 6174 Planarity : 0.005 0.070 7686 Dihedral : 14.475 176.787 7179 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 32.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.56 % Favored : 93.23 % Rotamer: Outliers : 0.02 % Allowed : 0.41 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % 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: -0.44 (0.11), residues: 5522 helix: 1.00 (0.11), residues: 2268 sheet: -0.92 (0.18), residues: 745 loop : -1.28 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP B 143 HIS 0.013 0.002 HIS E 153 PHE 0.049 0.003 PHE C 67 TYR 0.041 0.003 TYR B 905 ARG 0.024 0.001 ARG F 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 783 time to evaluate : 4.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 ASN cc_start: 0.8933 (t0) cc_final: 0.8508 (m-40) REVERT: A 635 MET cc_start: 0.8723 (ppp) cc_final: 0.8352 (ppp) REVERT: A 671 GLN cc_start: 0.8811 (mt0) cc_final: 0.8286 (mt0) REVERT: A 675 SER cc_start: 0.9661 (m) cc_final: 0.9381 (p) REVERT: A 695 TYR cc_start: 0.9084 (m-80) cc_final: 0.8682 (m-80) REVERT: A 726 TRP cc_start: 0.8781 (m-90) cc_final: 0.7282 (m-90) REVERT: A 782 ASP cc_start: 0.8316 (m-30) cc_final: 0.8086 (m-30) REVERT: A 830 MET cc_start: 0.8557 (mmp) cc_final: 0.7741 (mmp) REVERT: A 995 TYR cc_start: 0.9013 (t80) cc_final: 0.8727 (t80) REVERT: A 1306 TYR cc_start: 0.6951 (m-80) cc_final: 0.6710 (m-80) REVERT: A 1471 GLU cc_start: 0.8237 (tp30) cc_final: 0.7602 (tp30) REVERT: A 1568 ASN cc_start: 0.9030 (m110) cc_final: 0.8803 (m110) REVERT: B 25 PHE cc_start: 0.8543 (m-10) cc_final: 0.8121 (m-10) REVERT: B 215 MET cc_start: 0.8518 (mmm) cc_final: 0.8306 (mmm) REVERT: B 373 MET cc_start: 0.8992 (mmm) cc_final: 0.8603 (mmm) REVERT: B 411 MET cc_start: 0.8977 (mmp) cc_final: 0.8545 (mmp) REVERT: B 415 GLU cc_start: 0.8660 (tp30) cc_final: 0.8286 (tp30) REVERT: B 500 PHE cc_start: 0.9309 (m-80) cc_final: 0.9040 (m-80) REVERT: B 528 LEU cc_start: 0.9696 (mt) cc_final: 0.9477 (mp) REVERT: B 542 LEU cc_start: 0.9182 (tp) cc_final: 0.8966 (tp) REVERT: B 672 MET cc_start: 0.8857 (ptp) cc_final: 0.8648 (ptp) REVERT: B 715 ASN cc_start: 0.9188 (m110) cc_final: 0.8939 (m110) REVERT: B 734 CYS cc_start: 0.8246 (p) cc_final: 0.7984 (p) REVERT: B 740 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8215 (ttpp) REVERT: B 742 TYR cc_start: 0.8250 (m-10) cc_final: 0.7639 (m-10) REVERT: B 763 ASP cc_start: 0.8201 (t0) cc_final: 0.7680 (t0) REVERT: B 782 ASP cc_start: 0.8907 (p0) cc_final: 0.8531 (p0) REVERT: B 886 ASN cc_start: 0.8307 (m110) cc_final: 0.8093 (m110) REVERT: B 958 MET cc_start: 0.8793 (pmm) cc_final: 0.8199 (pmm) REVERT: B 1039 MET cc_start: 0.7946 (tmm) cc_final: 0.7210 (tmm) REVERT: B 1084 THR cc_start: 0.8376 (p) cc_final: 0.8085 (p) REVERT: C 82 TYR cc_start: 0.8484 (m-10) cc_final: 0.7708 (m-10) REVERT: E 50 MET cc_start: 0.8277 (mpp) cc_final: 0.7937 (mpp) REVERT: E 82 PHE cc_start: 0.8634 (m-80) cc_final: 0.8277 (m-80) REVERT: E 213 ILE cc_start: 0.8626 (tt) cc_final: 0.8140 (pt) REVERT: F 118 LEU cc_start: 0.9378 (mt) cc_final: 0.9112 (mt) REVERT: F 145 ASP cc_start: 0.7729 (m-30) cc_final: 0.7469 (m-30) REVERT: H 22 LYS cc_start: 0.8416 (ttpt) cc_final: 0.7913 (ptmt) REVERT: I 39 LYS cc_start: 0.8928 (mptt) cc_final: 0.8706 (mmtm) REVERT: I 94 MET cc_start: 0.1181 (mmt) cc_final: 0.0903 (tpp) REVERT: J 16 ASP cc_start: 0.8477 (p0) cc_final: 0.8035 (p0) REVERT: J 41 LEU cc_start: 0.8521 (mp) cc_final: 0.8190 (mp) REVERT: J 58 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8567 (tm-30) REVERT: J 60 PHE cc_start: 0.8806 (m-10) cc_final: 0.8585 (m-10) REVERT: K 135 PHE cc_start: 0.8310 (t80) cc_final: 0.7461 (t80) REVERT: L 27 LEU cc_start: 0.7839 (tp) cc_final: 0.7334 (tp) REVERT: L 33 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8898 (tm-30) REVERT: N 27 ASP cc_start: 0.9314 (t0) cc_final: 0.8777 (t70) REVERT: O 156 MET cc_start: 0.6995 (mmt) cc_final: 0.6527 (mmt) REVERT: O 433 LYS cc_start: 0.6193 (pptt) cc_final: 0.5534 (pptt) outliers start: 1 outliers final: 0 residues processed: 784 average time/residue: 0.5739 time to fit residues: 728.8860 Evaluate side-chains 598 residues out of total 4879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 272 optimal weight: 0.9990 chunk 352 optimal weight: 8.9990 chunk 473 optimal weight: 50.0000 chunk 136 optimal weight: 3.9990 chunk 409 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 444 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 456 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN A 993 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** A1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN O 451 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074013 restraints weight = 200671.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.075389 restraints weight = 160162.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.075495 restraints weight = 121629.812| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1231 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1232 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.9275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.937 44412 Z= 0.486 Angle : 0.704 20.141 60002 Z= 0.369 Chirality : 0.046 0.340 6174 Planarity : 0.005 0.084 7686 Dihedral : 14.255 177.661 7179 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % 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: -0.13 (0.11), residues: 5522 helix: 1.29 (0.11), residues: 2260 sheet: -0.82 (0.19), residues: 708 loop : -1.11 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP B 143 HIS 0.014 0.001 HIS E 153 PHE 0.035 0.002 PHE B 440 TYR 0.038 0.002 TYR B 905 ARG 0.021 0.001 ARG B 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13731.13 seconds wall clock time: 245 minutes 59.50 seconds (14759.50 seconds total)