Starting phenix.real_space_refine on Fri Aug 9 20:18:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c79_30296/08_2024/7c79_30296.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c79_30296/08_2024/7c79_30296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c79_30296/08_2024/7c79_30296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c79_30296/08_2024/7c79_30296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c79_30296/08_2024/7c79_30296.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c79_30296/08_2024/7c79_30296.cif" } resolution = 2.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 331 5.49 5 Mg 1 5.21 5 S 108 5.16 5 C 16022 2.51 5 N 4808 2.21 5 O 6053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B ARG 549": "NH1" <-> "NH2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 712": "OD1" <-> "OD2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 771": "OE1" <-> "OE2" Residue "B TYR 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 788": "OD1" <-> "OD2" Residue "B ASP 807": "OD1" <-> "OD2" Residue "B ASP 809": "OD1" <-> "OD2" Residue "B ARG 853": "NH1" <-> "NH2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "D ASP 10": "OD1" <-> "OD2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "E ARG 7": "NH1" <-> "NH2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "F TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 63": "OD1" <-> "OD2" Residue "F TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ASP 116": "OD1" <-> "OD2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "H ASP 22": "OD1" <-> "OD2" Residue "H TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "H ASP 129": "OD1" <-> "OD2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 64": "OD1" <-> "OD2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 68": "NH1" <-> "NH2" Residue "I ASP 74": "OD1" <-> "OD2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I ASP 127": "OD1" <-> "OD2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "I TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 166": "OD1" <-> "OD2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I ARG 202": "NH1" <-> "NH2" Residue "I ASP 219": "OD1" <-> "OD2" Residue "I ARG 237": "NH1" <-> "NH2" Residue "J ASP 4": "OD1" <-> "OD2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 83": "NH1" <-> "NH2" Residue "J ASP 90": "OD1" <-> "OD2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 127": "OD1" <-> "OD2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "J ARG 187": "NH1" <-> "NH2" Residue "J ASP 227": "OD1" <-> "OD2" Residue "J ASP 267": "OD1" <-> "OD2" Residue "J ASP 268": "OD1" <-> "OD2" Residue "J ARG 277": "NH1" <-> "NH2" Residue "J ASP 280": "OD1" <-> "OD2" Residue "J ARG 290": "NH1" <-> "NH2" Residue "K ARG 12": "NH1" <-> "NH2" Residue "K ARG 30": "NH1" <-> "NH2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "L ARG 16": "NH1" <-> "NH2" Residue "L GLU 40": "OE1" <-> "OE2" Residue "L ASP 64": "OD1" <-> "OD2" Residue "L PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27324 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 7008 Classifications: {'RNA': 331} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 24, 'rna3p_pur': 140, 'rna3p_pyr': 147} Link IDs: {'rna2p': 44, 'rna3p': 286} Chain breaks: 1 Chain: "B" Number of atoms: 6453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6453 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 37, 'TRANS': 755} Chain breaks: 3 Chain: "C" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1246 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 11, 'TRANS': 140} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2086 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1135 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "F" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1271 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2253 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "K" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 840 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1110 Classifications: {'peptide': 131} Link IDs: {'TRANS': 130} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" 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 25908 SG CYS K 64 54.461 52.784 52.287 1.00118.09 S Time building chain proxies: 18.29, per 1000 atoms: 0.67 Number of scatterers: 27324 At special positions: 0 Unit cell: (141.9, 133.1, 210.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 108 16.00 P 331 15.00 Mg 1 11.99 O 6053 8.00 N 4808 7.00 C 16022 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: 13.63 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 200 " pdb="ZN ZN K 200 " - pdb=" SG CYS K 64 " 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 17 sheets defined 45.1% alpha, 16.4% beta 41 base pairs and 135 stacking pairs defined. Time for finding SS restraints: 9.17 Creating SS restraints... Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.896A pdb=" N ARG B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 78 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 143 through 163 removed outlier: 3.637A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.642A pdb=" N LYS B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 removed outlier: 3.814A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.606A pdb=" N HIS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.686A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.519A pdb=" N ARG B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.261A pdb=" N GLN B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.761A pdb=" N SER B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.928A pdb=" N MET B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 471 through 479 removed outlier: 4.220A pdb=" N ILE B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 564 through 574 removed outlier: 3.742A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 593 removed outlier: 3.712A pdb=" N ASN B 593 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 removed outlier: 3.505A pdb=" N TYR B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 removed outlier: 4.065A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 718 removed outlier: 3.602A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 789 through 798 removed outlier: 3.500A pdb=" N LEU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 850 Processing helix chain 'C' and resid 40 through 56 removed outlier: 3.990A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 3.579A pdb=" N LEU C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.341A pdb=" N GLN C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.916A pdb=" N LYS D 15 " --> pdb=" O CYS D 11 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 26 removed outlier: 3.743A pdb=" N ASN D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 110 removed outlier: 3.697A pdb=" N ILE D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.605A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.608A pdb=" N TYR D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER D 132 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 126 through 133' Processing helix chain 'D' and resid 135 through 155 Proline residue: D 141 - end of helix removed outlier: 3.849A pdb=" N GLU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 273 through 279 removed outlier: 4.012A pdb=" N ILE D 277 " --> pdb=" O MET D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.919A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 122 through 146 removed outlier: 3.738A pdb=" N ILE E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 4.077A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.791A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 removed outlier: 3.877A pdb=" N LYS F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.898A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 85 removed outlier: 3.694A pdb=" N ASP G 84 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 30 through 46 removed outlier: 3.782A pdb=" N TRP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 3.534A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.729A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 69 through 77 removed outlier: 3.610A pdb=" N ASP I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.978A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE I 104 " --> pdb=" O ILE I 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 104' Processing helix chain 'I' and resid 113 through 123 removed outlier: 3.575A pdb=" N LEU I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN I 123 " --> pdb=" O LEU I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 153 removed outlier: 3.592A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG I 152 " --> pdb=" O SER I 148 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY I 153 " --> pdb=" O CYS I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.643A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 185 removed outlier: 4.236A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 3.578A pdb=" N SER I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 37 removed outlier: 3.636A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 4.306A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 3.834A pdb=" N ILE J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 Processing helix chain 'J' and resid 142 through 153 removed outlier: 4.074A pdb=" N ILE J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.781A pdb=" N LEU J 164 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 removed outlier: 4.098A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.810A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 242 removed outlier: 3.502A pdb=" N LEU J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA J 229 " --> pdb=" O MET J 225 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER J 230 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN J 240 " --> pdb=" O GLY J 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 removed outlier: 3.524A pdb=" N LYS K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 Processing helix chain 'K' and resid 29 through 48 removed outlier: 3.686A pdb=" N TYR K 47 " --> pdb=" O SER K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 58 removed outlier: 4.538A pdb=" N GLY K 58 " --> pdb=" O GLN K 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 26 removed outlier: 3.521A pdb=" N LEU L 17 " --> pdb=" O GLN L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 58 removed outlier: 3.686A pdb=" N GLN L 58 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 79 removed outlier: 4.000A pdb=" N TRP L 67 " --> pdb=" O LYS L 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL L 68 " --> pdb=" O ASP L 64 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE L 79 " --> pdb=" O GLN L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 96 removed outlier: 4.415A pdb=" N ARG L 84 " --> pdb=" O ARG L 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE L 93 " --> pdb=" O PHE L 89 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY L 96 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 131 removed outlier: 4.025A pdb=" N THR L 104 " --> pdb=" O THR L 100 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU L 115 " --> pdb=" O ASN L 111 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR L 125 " --> pdb=" O GLU L 121 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU L 126 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY L 131 " --> pdb=" O PHE L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.570A pdb=" N LEU B 57 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 33 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.061A pdb=" N GLY B 216 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 350 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN B 342 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 358 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE B 334 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 250 through 254 removed outlier: 6.546A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 450 removed outlier: 3.589A pdb=" N PHE B 448 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 762 through 769 removed outlier: 4.699A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN B 835 " --> pdb=" O TYR B 829 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR B 829 " --> pdb=" O ASN B 835 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET B 837 " --> pdb=" O GLY B 827 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY B 827 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 839 " --> pdb=" O THR B 825 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE B 823 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE B 821 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.970A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 246 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 234 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.970A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 246 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 234 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AB1, first strand: chain 'E' and resid 73 through 78 removed outlier: 6.764A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.103A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 121 " --> pdb=" O GLY F 4 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 138 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER F 83 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.103A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 121 " --> pdb=" O GLY F 4 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AB5, first strand: chain 'H' and resid 55 through 61 removed outlier: 8.815A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 103 " --> pdb=" O TYR H 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.523A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE I 41 " --> pdb=" O TYR I 81 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ARG I 83 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE I 43 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR I 85 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE I 45 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE I 87 " --> pdb=" O PHE I 45 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL I 47 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU I 129 " --> pdb=" O GLU I 157 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL I 159 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.181A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 103 through 105 888 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 135 stacking parallelities Total time for adding SS restraints: 11.61 Time building geometry restraints manager: 14.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7360 1.34 - 1.46: 7340 1.46 - 1.58: 12992 1.58 - 1.70: 660 1.70 - 1.82: 162 Bond restraints: 28514 Sorted by residual: bond pdb=" C ASN B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 1.337 1.361 -0.024 9.80e-03 1.04e+04 6.24e+00 bond pdb=" CA ILE C 58 " pdb=" CB ILE C 58 " ideal model delta sigma weight residual 1.553 1.539 0.014 7.40e-03 1.83e+04 3.40e+00 bond pdb=" C PHE B 598 " pdb=" N PRO B 599 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.38e+00 bond pdb=" C CYS C 94 " pdb=" N ASN C 95 " ideal model delta sigma weight residual 1.327 1.342 -0.014 9.40e-03 1.13e+04 2.37e+00 bond pdb=" CB GLN C 48 " pdb=" CG GLN C 48 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 ... (remaining 28509 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.35: 2284 106.35 - 113.30: 16145 113.30 - 120.25: 10311 120.25 - 127.20: 10512 127.20 - 134.15: 805 Bond angle restraints: 40057 Sorted by residual: angle pdb=" N PHE C 27 " pdb=" CA PHE C 27 " pdb=" C PHE C 27 " ideal model delta sigma weight residual 112.93 106.98 5.95 1.33e+00 5.65e-01 2.00e+01 angle pdb=" N ASN C 95 " pdb=" CA ASN C 95 " pdb=" C ASN C 95 " ideal model delta sigma weight residual 108.19 113.84 -5.65 1.29e+00 6.01e-01 1.92e+01 angle pdb=" C ILE B 202 " pdb=" N LYS B 203 " pdb=" CA LYS B 203 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.79e+01 angle pdb=" N HIS K 22 " pdb=" CA HIS K 22 " pdb=" C HIS K 22 " ideal model delta sigma weight residual 112.13 117.65 -5.52 1.37e+00 5.33e-01 1.62e+01 angle pdb=" CA GLN C 45 " pdb=" CB GLN C 45 " pdb=" CG GLN C 45 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 ... (remaining 40052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 16800 34.68 - 69.37: 868 69.37 - 104.05: 85 104.05 - 138.74: 5 138.74 - 173.42: 11 Dihedral angle restraints: 17769 sinusoidal: 10381 harmonic: 7388 Sorted by residual: dihedral pdb=" C4' U A 143 " pdb=" C3' U A 143 " pdb=" C2' U A 143 " pdb=" C1' U A 143 " ideal model delta sinusoidal sigma weight residual -35.00 33.74 -68.74 1 8.00e+00 1.56e-02 9.56e+01 dihedral pdb=" C5' U A 143 " pdb=" C4' U A 143 " pdb=" C3' U A 143 " pdb=" O3' U A 143 " ideal model delta sinusoidal sigma weight residual 147.00 83.24 63.76 1 8.00e+00 1.56e-02 8.37e+01 dihedral pdb=" O4' U A 143 " pdb=" C2' U A 143 " pdb=" C1' U A 143 " pdb=" C3' U A 143 " ideal model delta sinusoidal sigma weight residual -35.00 22.78 -57.78 1 8.00e+00 1.56e-02 7.00e+01 ... (remaining 17766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4359 0.060 - 0.119: 391 0.119 - 0.179: 39 0.179 - 0.239: 2 0.239 - 0.299: 1 Chirality restraints: 4792 Sorted by residual: chirality pdb=" C3' U A 143 " pdb=" C4' U A 143 " pdb=" O3' U A 143 " pdb=" C2' U A 143 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' U A 143 " pdb=" C3' U A 143 " pdb=" O2' U A 143 " pdb=" C1' U A 143 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C3' G A 15 " pdb=" C4' G A 15 " pdb=" O3' G A 15 " pdb=" C2' G A 15 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 4789 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 100 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 101 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 118 " 0.018 2.00e-02 2.50e+03 1.42e-02 5.05e+00 pdb=" CG TRP H 118 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP H 118 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 118 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 118 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 118 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 118 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 118 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 118 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 14 " -0.027 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 A A 14 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A A 14 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 14 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 14 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A A 14 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A 14 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 14 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 14 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 14 " 0.003 2.00e-02 2.50e+03 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 180 2.56 - 3.14: 20198 3.14 - 3.73: 43250 3.73 - 4.31: 59736 4.31 - 4.90: 92354 Nonbonded interactions: 215718 Sorted by model distance: nonbonded pdb=" O GLN B 587 " pdb=" OH TYR B 597 " model vdw 1.974 3.040 nonbonded pdb=" O2' A A 31 " pdb=" OP1 G A 264 " model vdw 2.146 3.040 nonbonded pdb=" O2' A A 37 " pdb=" O VAL G 35 " model vdw 2.178 3.040 nonbonded pdb=" O ASP J 89 " pdb=" OG SER J 113 " model vdw 2.196 3.040 nonbonded pdb=" OP1 A A 86 " pdb="MG MG A 401 " model vdw 2.196 2.170 ... (remaining 215713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 94.350 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 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 : 0.002 0.042 28514 Z= 0.146 Angle : 0.593 9.361 40057 Z= 0.359 Chirality : 0.035 0.299 4792 Planarity : 0.003 0.059 3861 Dihedral : 18.303 173.421 12969 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.15), residues: 2485 helix: -1.14 (0.15), residues: 1016 sheet: -0.99 (0.25), residues: 389 loop : -3.23 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 118 HIS 0.009 0.001 HIS B 371 PHE 0.012 0.001 PHE F 118 TYR 0.015 0.001 TYR D 136 ARG 0.006 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 642 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8201 (mmm) cc_final: 0.7964 (mmp) REVERT: B 209 MET cc_start: 0.7356 (mtp) cc_final: 0.7148 (mtt) REVERT: B 362 GLN cc_start: 0.7857 (tt0) cc_final: 0.7297 (tm-30) REVERT: B 603 PRO cc_start: 0.7935 (Cg_endo) cc_final: 0.7644 (Cg_exo) REVERT: D 72 GLN cc_start: 0.7585 (mp10) cc_final: 0.7363 (mp10) REVERT: D 135 GLN cc_start: 0.6657 (mm110) cc_final: 0.6230 (mm-40) REVERT: F 63 ASP cc_start: 0.7633 (p0) cc_final: 0.7371 (p0) REVERT: F 131 GLU cc_start: 0.7125 (pt0) cc_final: 0.6875 (pt0) REVERT: F 132 ARG cc_start: 0.7167 (mpp80) cc_final: 0.6886 (mpp80) REVERT: H 129 ASP cc_start: 0.7361 (t0) cc_final: 0.7146 (t0) REVERT: I 220 ARG cc_start: 0.7268 (mmt180) cc_final: 0.7060 (mpt-90) REVERT: J 223 LYS cc_start: 0.6768 (tptt) cc_final: 0.6295 (ttpp) REVERT: K 28 ASN cc_start: 0.7736 (t0) cc_final: 0.7451 (m-40) REVERT: L 122 ILE cc_start: 0.6252 (mm) cc_final: 0.5756 (mm) outliers start: 2 outliers final: 5 residues processed: 644 average time/residue: 1.4673 time to fit residues: 1087.5112 Evaluate side-chains 338 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 333 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain H residue 58 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 256 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 HIS B 201 ASN B 218 ASN B 323 ASN B 335 GLN B 342 ASN B 380 ASN B 437 HIS B 508 ASN ** B 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 595 GLN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 ASN ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS C 107 GLN D 99 ASN D 135 GLN E 50 GLN E 134 ASN F 87 HIS F 89 GLN F 153 HIS G 28 GLN G 49 ASN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN G 85 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN I 6 ASN I 132 GLN I 213 ASN K 19 ASN K 108 ASN L 47 GLN L 90 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 28514 Z= 0.384 Angle : 0.812 10.837 40057 Z= 0.419 Chirality : 0.046 0.275 4792 Planarity : 0.006 0.072 3861 Dihedral : 19.741 175.748 7810 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.60 % Rotamer: Outliers : 5.71 % Allowed : 15.29 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.93 (0.16), residues: 2485 helix: -0.24 (0.15), residues: 1053 sheet: -0.24 (0.26), residues: 385 loop : -2.84 (0.16), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP H 118 HIS 0.009 0.002 HIS K 41 PHE 0.027 0.003 PHE I 45 TYR 0.056 0.003 TYR B 597 ARG 0.012 0.001 ARG B 574 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 355 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6544 (mtm-85) REVERT: B 112 MET cc_start: 0.8569 (mmm) cc_final: 0.8141 (mmt) REVERT: B 117 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7548 (mm) REVERT: B 145 LYS cc_start: 0.7666 (ptmt) cc_final: 0.7178 (mmtm) REVERT: B 179 CYS cc_start: 0.8189 (m) cc_final: 0.7939 (t) REVERT: B 191 MET cc_start: 0.8536 (mpt) cc_final: 0.8318 (mpt) REVERT: B 362 GLN cc_start: 0.7800 (tt0) cc_final: 0.7352 (tm-30) REVERT: B 430 MET cc_start: 0.8040 (ttm) cc_final: 0.7749 (ttp) REVERT: B 714 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6827 (tm-30) REVERT: C 45 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8663 (pm20) REVERT: D 72 GLN cc_start: 0.7784 (mp10) cc_final: 0.7415 (tp-100) REVERT: D 96 CYS cc_start: 0.7839 (t) cc_final: 0.7624 (m) REVERT: D 164 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8076 (t80) REVERT: D 269 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6792 (ttp-170) REVERT: D 273 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6902 (mpp) REVERT: E 22 VAL cc_start: 0.8642 (t) cc_final: 0.8198 (m) REVERT: E 57 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8320 (p) REVERT: F 15 ASP cc_start: 0.7870 (t0) cc_final: 0.7638 (t0) REVERT: F 89 GLN cc_start: 0.8147 (tt0) cc_final: 0.7528 (tt0) REVERT: F 125 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6846 (mtp180) REVERT: F 132 ARG cc_start: 0.7404 (mpp80) cc_final: 0.7137 (mpp80) REVERT: G 88 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7826 (mtpp) REVERT: G 89 LYS cc_start: 0.8101 (tttt) cc_final: 0.7892 (ttpt) REVERT: H 44 ARG cc_start: 0.7845 (tpm170) cc_final: 0.7519 (tpm170) REVERT: H 117 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8646 (mm) REVERT: I 140 PHE cc_start: 0.7494 (t80) cc_final: 0.7238 (t80) REVERT: J 1 MET cc_start: 0.7496 (mmm) cc_final: 0.7261 (mmm) REVERT: J 223 LYS cc_start: 0.7373 (tptt) cc_final: 0.6661 (ttpt) REVERT: K 28 ASN cc_start: 0.8171 (t0) cc_final: 0.7831 (t0) REVERT: K 90 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6399 (mm) REVERT: L 100 THR cc_start: 0.8234 (t) cc_final: 0.7950 (t) REVERT: L 103 CYS cc_start: 0.7621 (p) cc_final: 0.7135 (p) outliers start: 131 outliers final: 40 residues processed: 452 average time/residue: 1.3497 time to fit residues: 710.6038 Evaluate side-chains 318 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 267 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 201 CYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 200 GLU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 70 optimal weight: 0.0970 chunk 256 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 254 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS B 266 GLN B 570 HIS B 585 GLN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS D 197 GLN E 50 GLN F 52 ASN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN I 172 GLN J 40 HIS L 97 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28514 Z= 0.180 Angle : 0.613 10.599 40057 Z= 0.313 Chirality : 0.039 0.228 4792 Planarity : 0.004 0.058 3861 Dihedral : 19.401 177.113 7802 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 4.44 % Allowed : 18.99 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.31 (0.16), residues: 2485 helix: 0.43 (0.16), residues: 1045 sheet: -0.01 (0.25), residues: 405 loop : -2.67 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP H 118 HIS 0.018 0.001 HIS F 153 PHE 0.023 0.001 PHE B 586 TYR 0.022 0.002 TYR J 160 ARG 0.010 0.001 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 314 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8529 (mmm) cc_final: 0.8231 (mmp) REVERT: B 191 MET cc_start: 0.8431 (mpt) cc_final: 0.8038 (mpt) REVERT: B 209 MET cc_start: 0.7226 (mtm) cc_final: 0.6914 (mtt) REVERT: B 325 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7469 (tpp80) REVERT: B 370 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6968 (pp) REVERT: B 430 MET cc_start: 0.7998 (ttm) cc_final: 0.7749 (ttp) REVERT: B 433 MET cc_start: 0.8305 (mtm) cc_final: 0.8049 (mtp) REVERT: B 603 PRO cc_start: 0.8192 (Cg_endo) cc_final: 0.7964 (Cg_exo) REVERT: B 714 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6752 (tm-30) REVERT: B 811 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8045 (tmtm) REVERT: C 45 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8463 (pm20) REVERT: D 72 GLN cc_start: 0.7800 (mp10) cc_final: 0.7480 (tp-100) REVERT: D 206 LYS cc_start: 0.7810 (mttt) cc_final: 0.7432 (mttm) REVERT: D 219 GLU cc_start: 0.5557 (mp0) cc_final: 0.5309 (mp0) REVERT: D 269 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6765 (ttp-170) REVERT: E 19 ASP cc_start: 0.6604 (t0) cc_final: 0.6396 (t0) REVERT: E 22 VAL cc_start: 0.8671 (t) cc_final: 0.8269 (m) REVERT: E 42 ASP cc_start: 0.8079 (m-30) cc_final: 0.7732 (t0) REVERT: F 89 GLN cc_start: 0.7819 (tt0) cc_final: 0.7319 (mt0) REVERT: F 132 ARG cc_start: 0.7305 (mpp80) cc_final: 0.7051 (mpp80) REVERT: G 58 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5365 (tm-30) REVERT: H 44 ARG cc_start: 0.7763 (tpm170) cc_final: 0.7434 (tpm170) REVERT: I 140 PHE cc_start: 0.7360 (t80) cc_final: 0.7120 (t80) REVERT: I 227 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6451 (m-30) REVERT: I 238 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7720 (tm) REVERT: J 1 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7285 (mmm) REVERT: J 136 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6290 (ppt170) REVERT: J 196 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6956 (mtm) REVERT: J 223 LYS cc_start: 0.7348 (tptt) cc_final: 0.6444 (ttpt) REVERT: J 240 ASN cc_start: 0.5873 (OUTLIER) cc_final: 0.5543 (m-40) REVERT: K 28 ASN cc_start: 0.8067 (t0) cc_final: 0.7697 (m-40) REVERT: L 97 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6708 (mt0) REVERT: L 100 THR cc_start: 0.7975 (t) cc_final: 0.7685 (t) REVERT: L 103 CYS cc_start: 0.6674 (p) cc_final: 0.6227 (p) outliers start: 102 outliers final: 28 residues processed: 391 average time/residue: 1.3256 time to fit residues: 606.1812 Evaluate side-chains 320 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 279 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 109 CYS Chi-restraints excluded: chain L residue 97 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 HIS B 385 HIS B 466 GLN B 505 ASN B 506 ASN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS E 50 GLN G 58 GLN I 172 GLN ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 HIS K 108 ASN L 97 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28514 Z= 0.198 Angle : 0.614 11.523 40057 Z= 0.311 Chirality : 0.039 0.228 4792 Planarity : 0.004 0.056 3861 Dihedral : 19.311 176.745 7802 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.05 % Allowed : 21.17 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.96 (0.16), residues: 2485 helix: 0.66 (0.16), residues: 1056 sheet: 0.17 (0.25), residues: 402 loop : -2.43 (0.17), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP H 118 HIS 0.005 0.001 HIS F 153 PHE 0.019 0.001 PHE H 77 TYR 0.022 0.002 TYR D 92 ARG 0.006 0.001 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 295 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6924 (mtm-85) REVERT: B 112 MET cc_start: 0.8552 (mmm) cc_final: 0.8309 (mmp) REVERT: B 145 LYS cc_start: 0.7538 (ptmt) cc_final: 0.7111 (mmtm) REVERT: B 191 MET cc_start: 0.8427 (mpt) cc_final: 0.8085 (mpt) REVERT: B 209 MET cc_start: 0.7288 (mtm) cc_final: 0.6922 (mtt) REVERT: B 370 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7092 (pp) REVERT: B 430 MET cc_start: 0.8039 (ttm) cc_final: 0.7764 (ttp) REVERT: B 487 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7153 (mp) REVERT: B 678 ASP cc_start: 0.5509 (OUTLIER) cc_final: 0.5237 (m-30) REVERT: B 714 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6731 (tm-30) REVERT: B 811 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8067 (tmtm) REVERT: B 845 HIS cc_start: 0.7252 (t70) cc_final: 0.7019 (t70) REVERT: C 45 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: C 117 MET cc_start: 0.7898 (mpm) cc_final: 0.7317 (mtp) REVERT: D 72 GLN cc_start: 0.7758 (mp10) cc_final: 0.7443 (tp-100) REVERT: D 135 GLN cc_start: 0.7508 (mm110) cc_final: 0.7216 (mm-40) REVERT: D 206 LYS cc_start: 0.7863 (mttt) cc_final: 0.7507 (mttm) REVERT: D 269 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6826 (ttp-170) REVERT: E 22 VAL cc_start: 0.8713 (t) cc_final: 0.8334 (m) REVERT: E 142 LYS cc_start: 0.8078 (mppt) cc_final: 0.7834 (mppt) REVERT: F 89 GLN cc_start: 0.7854 (tt0) cc_final: 0.7357 (mt0) REVERT: F 125 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6814 (mtp180) REVERT: F 132 ARG cc_start: 0.7425 (mpp80) cc_final: 0.7179 (mpp80) REVERT: H 43 LYS cc_start: 0.6891 (tppt) cc_final: 0.6666 (tptp) REVERT: I 238 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7583 (tm) REVERT: J 1 MET cc_start: 0.7572 (mmm) cc_final: 0.7331 (mmm) REVERT: J 136 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6368 (ppt170) REVERT: J 196 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7108 (mtm) REVERT: J 223 LYS cc_start: 0.7508 (tptt) cc_final: 0.6550 (ttpp) REVERT: J 240 ASN cc_start: 0.5816 (OUTLIER) cc_final: 0.5473 (m-40) REVERT: L 100 THR cc_start: 0.8005 (t) cc_final: 0.7744 (t) REVERT: L 103 CYS cc_start: 0.7027 (p) cc_final: 0.6748 (p) outliers start: 93 outliers final: 42 residues processed: 362 average time/residue: 1.2825 time to fit residues: 542.8626 Evaluate side-chains 324 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 270 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 201 CYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 109 CYS Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN B 335 GLN B 385 HIS B 505 ASN B 612 ASN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS F 37 ASN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 28514 Z= 0.243 Angle : 0.645 12.131 40057 Z= 0.328 Chirality : 0.040 0.227 4792 Planarity : 0.005 0.075 3861 Dihedral : 19.288 178.470 7801 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 4.40 % Allowed : 21.34 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.81 (0.17), residues: 2485 helix: 0.77 (0.16), residues: 1060 sheet: 0.23 (0.25), residues: 393 loop : -2.31 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP H 118 HIS 0.005 0.001 HIS K 41 PHE 0.025 0.002 PHE K 60 TYR 0.022 0.002 TYR J 160 ARG 0.009 0.001 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 288 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6923 (mtm-85) REVERT: B 112 MET cc_start: 0.8589 (mmm) cc_final: 0.8362 (mmp) REVERT: B 145 LYS cc_start: 0.7755 (ptmt) cc_final: 0.7380 (mmtm) REVERT: B 191 MET cc_start: 0.8373 (mpt) cc_final: 0.8113 (mpt) REVERT: B 193 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7622 (ptpp) REVERT: B 234 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6381 (pt0) REVERT: B 430 MET cc_start: 0.8105 (ttm) cc_final: 0.7813 (ttp) REVERT: B 487 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7259 (mp) REVERT: B 714 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6718 (tm-30) REVERT: B 811 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8167 (tmtm) REVERT: B 845 HIS cc_start: 0.7322 (t70) cc_final: 0.7040 (t70) REVERT: C 45 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: C 117 MET cc_start: 0.7810 (mpm) cc_final: 0.7203 (mtp) REVERT: D 72 GLN cc_start: 0.7772 (mp10) cc_final: 0.7570 (tp-100) REVERT: D 139 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7118 (t80) REVERT: D 219 GLU cc_start: 0.5783 (mp0) cc_final: 0.5466 (mp0) REVERT: D 269 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6821 (ttp-170) REVERT: E 19 ASP cc_start: 0.7108 (t0) cc_final: 0.6904 (t0) REVERT: E 22 VAL cc_start: 0.8707 (t) cc_final: 0.8342 (m) REVERT: E 98 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6650 (ttm) REVERT: E 142 LYS cc_start: 0.8182 (mppt) cc_final: 0.7967 (mppt) REVERT: F 89 GLN cc_start: 0.7981 (tt0) cc_final: 0.7482 (mt0) REVERT: F 125 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6872 (mtp180) REVERT: F 132 ARG cc_start: 0.7414 (mpp80) cc_final: 0.7101 (mpp80) REVERT: G 28 GLN cc_start: 0.8591 (mt0) cc_final: 0.8380 (mt0) REVERT: H 9 TRP cc_start: 0.7507 (OUTLIER) cc_final: 0.6715 (p90) REVERT: H 25 ASP cc_start: 0.8125 (m-30) cc_final: 0.7718 (p0) REVERT: H 43 LYS cc_start: 0.7082 (tppt) cc_final: 0.6814 (tptp) REVERT: H 107 ARG cc_start: 0.6439 (tpp-160) cc_final: 0.6144 (mmp80) REVERT: H 120 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8487 (mtmp) REVERT: J 1 MET cc_start: 0.7629 (mmm) cc_final: 0.7398 (mmm) REVERT: J 100 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7187 (mm) REVERT: J 136 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6421 (ppt170) REVERT: J 196 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7563 (mtp) REVERT: K 28 ASN cc_start: 0.8048 (t0) cc_final: 0.7064 (p0) REVERT: K 89 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7094 (pt0) REVERT: L 100 THR cc_start: 0.8079 (t) cc_final: 0.7830 (t) REVERT: L 103 CYS cc_start: 0.7185 (p) cc_final: 0.6653 (p) outliers start: 101 outliers final: 49 residues processed: 359 average time/residue: 1.3341 time to fit residues: 559.6841 Evaluate side-chains 319 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 256 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 201 CYS Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 109 CYS Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.0170 chunk 245 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 272 optimal weight: 0.9990 chunk 226 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 0.4980 chunk 143 optimal weight: 4.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 HIS B 505 ASN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS E 89 HIS F 37 ASN ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 GLN L 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28514 Z= 0.164 Angle : 0.599 12.264 40057 Z= 0.302 Chirality : 0.038 0.223 4792 Planarity : 0.004 0.071 3861 Dihedral : 19.118 175.348 7801 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.14 % Allowed : 22.43 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.57 (0.17), residues: 2485 helix: 1.01 (0.16), residues: 1055 sheet: 0.38 (0.25), residues: 406 loop : -2.27 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP H 118 HIS 0.005 0.001 HIS G 56 PHE 0.026 0.001 PHE K 60 TYR 0.024 0.001 TYR K 36 ARG 0.010 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 301 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8552 (mmm) cc_final: 0.8125 (mmt) REVERT: B 145 LYS cc_start: 0.7638 (ptmt) cc_final: 0.7241 (mmtm) REVERT: B 209 MET cc_start: 0.7214 (mtm) cc_final: 0.6901 (mtt) REVERT: B 430 MET cc_start: 0.7989 (ttm) cc_final: 0.7727 (ttp) REVERT: B 678 ASP cc_start: 0.5539 (OUTLIER) cc_final: 0.5215 (m-30) REVERT: B 684 MET cc_start: 0.6451 (mmt) cc_final: 0.6249 (mmm) REVERT: B 714 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6664 (tm-30) REVERT: B 811 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8156 (tmtm) REVERT: B 845 HIS cc_start: 0.7259 (t70) cc_final: 0.7025 (t70) REVERT: C 45 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: C 117 MET cc_start: 0.7778 (mpm) cc_final: 0.7302 (mtp) REVERT: D 19 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8111 (p0) REVERT: D 72 GLN cc_start: 0.7721 (mp10) cc_final: 0.7506 (tp-100) REVERT: D 206 LYS cc_start: 0.7818 (mttt) cc_final: 0.7496 (mttm) REVERT: E 19 ASP cc_start: 0.7125 (t0) cc_final: 0.6923 (t0) REVERT: E 22 VAL cc_start: 0.8682 (t) cc_final: 0.8328 (m) REVERT: E 42 ASP cc_start: 0.8016 (t0) cc_final: 0.7673 (t0) REVERT: E 133 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7873 (ttt90) REVERT: F 89 GLN cc_start: 0.7756 (tt0) cc_final: 0.7363 (mt0) REVERT: F 132 ARG cc_start: 0.7195 (mpp80) cc_final: 0.6956 (mpp80) REVERT: H 9 TRP cc_start: 0.7577 (OUTLIER) cc_final: 0.7135 (p90) REVERT: H 25 ASP cc_start: 0.8059 (m-30) cc_final: 0.7772 (p0) REVERT: H 43 LYS cc_start: 0.7004 (tppt) cc_final: 0.6723 (tptp) REVERT: H 107 ARG cc_start: 0.6532 (tpp-160) cc_final: 0.6224 (mmp80) REVERT: H 117 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8632 (mm) REVERT: I 168 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8031 (mp10) REVERT: J 1 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7334 (mmm) REVERT: J 78 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7089 (pp) REVERT: J 136 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6347 (ppt170) REVERT: J 225 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.6265 (mtt) REVERT: K 1 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.5794 (mmt) REVERT: K 8 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7828 (ttpt) REVERT: K 28 ASN cc_start: 0.7903 (t0) cc_final: 0.7063 (p0) REVERT: L 100 THR cc_start: 0.7929 (t) cc_final: 0.7686 (t) REVERT: L 103 CYS cc_start: 0.7298 (p) cc_final: 0.6729 (p) REVERT: L 111 ASN cc_start: 0.7709 (t0) cc_final: 0.7416 (m-40) outliers start: 95 outliers final: 37 residues processed: 363 average time/residue: 1.2775 time to fit residues: 542.5893 Evaluate side-chains 309 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 260 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 109 CYS Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 229 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN B 385 HIS B 392 GLN B 492 ASN B 505 ASN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN L 75 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28514 Z= 0.224 Angle : 0.642 12.555 40057 Z= 0.326 Chirality : 0.039 0.222 4792 Planarity : 0.004 0.078 3861 Dihedral : 19.164 177.930 7801 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.61 % Allowed : 23.65 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2485 helix: 0.93 (0.16), residues: 1057 sheet: 0.33 (0.26), residues: 395 loop : -2.20 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP H 118 HIS 0.005 0.001 HIS B 371 PHE 0.014 0.001 PHE B 586 TYR 0.024 0.002 TYR J 160 ARG 0.011 0.001 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 269 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6916 (mtm-85) REVERT: B 112 MET cc_start: 0.8587 (mmm) cc_final: 0.8201 (mmt) REVERT: B 145 LYS cc_start: 0.7776 (ptmt) cc_final: 0.7409 (mmtm) REVERT: B 209 MET cc_start: 0.7382 (mtm) cc_final: 0.7177 (mtp) REVERT: B 370 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6905 (pp) REVERT: B 430 MET cc_start: 0.8080 (ttm) cc_final: 0.7807 (ttp) REVERT: B 510 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6873 (tp) REVERT: B 678 ASP cc_start: 0.5801 (OUTLIER) cc_final: 0.5448 (m-30) REVERT: B 684 MET cc_start: 0.6691 (mmt) cc_final: 0.6363 (mmm) REVERT: B 714 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6692 (tm-30) REVERT: B 811 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8160 (tmtm) REVERT: B 845 HIS cc_start: 0.7331 (t70) cc_final: 0.7041 (t70) REVERT: C 45 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8382 (pm20) REVERT: C 68 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8166 (mm) REVERT: C 117 MET cc_start: 0.7720 (mpm) cc_final: 0.7235 (mtp) REVERT: C 137 LYS cc_start: 0.7473 (tppp) cc_final: 0.7262 (tppp) REVERT: C 140 MET cc_start: 0.5530 (mtm) cc_final: 0.4488 (pmt) REVERT: D 19 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8183 (p0) REVERT: D 72 GLN cc_start: 0.7739 (mp10) cc_final: 0.7518 (tp-100) REVERT: D 139 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7331 (t80) REVERT: D 219 GLU cc_start: 0.6176 (mp0) cc_final: 0.5790 (mp0) REVERT: E 19 ASP cc_start: 0.7230 (t0) cc_final: 0.7008 (t0) REVERT: E 22 VAL cc_start: 0.8719 (t) cc_final: 0.8319 (m) REVERT: E 133 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7857 (ttt90) REVERT: F 89 GLN cc_start: 0.7928 (tt0) cc_final: 0.7487 (mt0) REVERT: F 109 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8187 (mp) REVERT: F 123 GLU cc_start: 0.7110 (tt0) cc_final: 0.6808 (tt0) REVERT: F 129 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7206 (mt0) REVERT: F 131 GLU cc_start: 0.7805 (pt0) cc_final: 0.7521 (pp20) REVERT: F 132 ARG cc_start: 0.7197 (mpp80) cc_final: 0.6870 (mpp80) REVERT: H 9 TRP cc_start: 0.7577 (OUTLIER) cc_final: 0.6770 (p90) REVERT: H 25 ASP cc_start: 0.8087 (m-30) cc_final: 0.7734 (p0) REVERT: H 43 LYS cc_start: 0.7118 (tppt) cc_final: 0.6831 (tptp) REVERT: I 168 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8078 (mp10) REVERT: J 136 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6366 (ppt170) REVERT: J 225 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6359 (mtp) REVERT: K 28 ASN cc_start: 0.7945 (t0) cc_final: 0.7236 (p0) REVERT: K 48 GLN cc_start: 0.7882 (pt0) cc_final: 0.7607 (pp30) REVERT: K 89 GLU cc_start: 0.6779 (pt0) cc_final: 0.6376 (pt0) REVERT: L 100 THR cc_start: 0.8012 (t) cc_final: 0.7768 (t) REVERT: L 103 CYS cc_start: 0.7231 (p) cc_final: 0.6762 (p) REVERT: L 111 ASN cc_start: 0.7659 (t0) cc_final: 0.7369 (m-40) outliers start: 83 outliers final: 41 residues processed: 327 average time/residue: 1.3044 time to fit residues: 500.0318 Evaluate side-chains 309 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 253 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 109 CYS Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 0.0570 chunk 81 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 172 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 HIS B 492 ASN B 505 ASN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN D 126 HIS G 28 GLN H 21 GLN H 27 HIS ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28514 Z= 0.174 Angle : 0.625 14.607 40057 Z= 0.314 Chirality : 0.038 0.218 4792 Planarity : 0.004 0.077 3861 Dihedral : 19.076 175.250 7801 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.22 % Allowed : 24.61 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.17), residues: 2485 helix: 1.09 (0.17), residues: 1050 sheet: 0.42 (0.25), residues: 406 loop : -2.17 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP H 118 HIS 0.004 0.001 HIS D 126 PHE 0.017 0.001 PHE B 586 TYR 0.025 0.001 TYR D 121 ARG 0.010 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 280 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6906 (mtm-85) REVERT: B 112 MET cc_start: 0.8549 (mmm) cc_final: 0.8175 (mmt) REVERT: B 145 LYS cc_start: 0.7778 (ptmt) cc_final: 0.7398 (mmtm) REVERT: B 209 MET cc_start: 0.7340 (mtm) cc_final: 0.6968 (mtt) REVERT: B 389 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8280 (mp) REVERT: B 430 MET cc_start: 0.8065 (ttm) cc_final: 0.7809 (ttp) REVERT: B 678 ASP cc_start: 0.5817 (OUTLIER) cc_final: 0.5457 (m-30) REVERT: B 714 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6651 (tm-30) REVERT: B 811 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8138 (tmtm) REVERT: B 845 HIS cc_start: 0.7295 (t70) cc_final: 0.7029 (t70) REVERT: C 45 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: C 68 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8315 (mm) REVERT: C 117 MET cc_start: 0.7745 (mpm) cc_final: 0.7521 (mtp) REVERT: C 140 MET cc_start: 0.5414 (mtm) cc_final: 0.4612 (pmt) REVERT: D 19 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8135 (p0) REVERT: D 72 GLN cc_start: 0.7673 (mp10) cc_final: 0.7450 (tp-100) REVERT: D 111 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8374 (mppt) REVERT: D 139 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7036 (t80) REVERT: D 219 GLU cc_start: 0.6007 (mp0) cc_final: 0.5609 (mp0) REVERT: E 42 ASP cc_start: 0.8086 (t0) cc_final: 0.7785 (t0) REVERT: E 133 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7994 (ttt90) REVERT: F 89 GLN cc_start: 0.7780 (tt0) cc_final: 0.7398 (mt0) REVERT: F 123 GLU cc_start: 0.7292 (tt0) cc_final: 0.7091 (tt0) REVERT: F 131 GLU cc_start: 0.7755 (pt0) cc_final: 0.7502 (pp20) REVERT: F 132 ARG cc_start: 0.7104 (mpp80) cc_final: 0.6688 (mpp80) REVERT: G 91 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6898 (mp0) REVERT: H 9 TRP cc_start: 0.7499 (OUTLIER) cc_final: 0.6731 (p90) REVERT: H 25 ASP cc_start: 0.8113 (m-30) cc_final: 0.7726 (p0) REVERT: H 43 LYS cc_start: 0.7056 (tppt) cc_final: 0.6815 (tptp) REVERT: I 168 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8104 (mp10) REVERT: J 136 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6326 (ppt170) REVERT: J 225 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6275 (mtp) REVERT: K 1 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.5541 (mmt) REVERT: K 28 ASN cc_start: 0.7747 (t0) cc_final: 0.7267 (p0) REVERT: K 48 GLN cc_start: 0.7857 (pt0) cc_final: 0.7575 (pp30) REVERT: K 89 GLU cc_start: 0.6841 (pt0) cc_final: 0.6316 (pt0) REVERT: L 84 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6943 (ttm170) REVERT: L 103 CYS cc_start: 0.7124 (p) cc_final: 0.6668 (p) REVERT: L 111 ASN cc_start: 0.7652 (t0) cc_final: 0.7314 (m-40) outliers start: 74 outliers final: 39 residues processed: 332 average time/residue: 1.2970 time to fit residues: 502.6407 Evaluate side-chains 307 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 109 CYS Chi-restraints excluded: chain L residue 84 ARG Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN B 385 HIS B 505 ASN B 595 GLN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS F 37 ASN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 27 HIS I 168 GLN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28514 Z= 0.233 Angle : 0.675 15.794 40057 Z= 0.341 Chirality : 0.040 0.218 4792 Planarity : 0.005 0.086 3861 Dihedral : 19.138 177.308 7801 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.35 % Allowed : 24.74 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.17), residues: 2485 helix: 0.99 (0.17), residues: 1056 sheet: 0.33 (0.26), residues: 393 loop : -2.13 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.002 TRP H 118 HIS 0.005 0.001 HIS H 27 PHE 0.014 0.001 PHE B 586 TYR 0.026 0.002 TYR J 160 ARG 0.010 0.001 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 266 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6905 (mtm-85) REVERT: B 112 MET cc_start: 0.8586 (mmm) cc_final: 0.8211 (mmt) REVERT: B 145 LYS cc_start: 0.7923 (ptmt) cc_final: 0.7635 (mmtm) REVERT: B 389 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8209 (mp) REVERT: B 430 MET cc_start: 0.8108 (ttm) cc_final: 0.7829 (ttp) REVERT: B 510 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6909 (tp) REVERT: B 678 ASP cc_start: 0.5789 (OUTLIER) cc_final: 0.5449 (m-30) REVERT: B 684 MET cc_start: 0.6986 (mmm) cc_final: 0.6687 (mmt) REVERT: B 714 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6682 (tm-30) REVERT: B 811 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8179 (tmtm) REVERT: C 68 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8236 (mm) REVERT: C 140 MET cc_start: 0.5487 (mtm) cc_final: 0.4624 (pmt) REVERT: D 19 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8166 (p0) REVERT: D 72 GLN cc_start: 0.7700 (mp10) cc_final: 0.7479 (tp-100) REVERT: D 111 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8385 (mppt) REVERT: D 219 GLU cc_start: 0.5745 (mp0) cc_final: 0.5413 (mp0) REVERT: D 269 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6618 (ttp-170) REVERT: E 42 ASP cc_start: 0.8316 (t0) cc_final: 0.8001 (t0) REVERT: E 133 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8047 (ttt90) REVERT: F 89 GLN cc_start: 0.7970 (tt0) cc_final: 0.7513 (mt0) REVERT: F 131 GLU cc_start: 0.7820 (pt0) cc_final: 0.7505 (pp20) REVERT: F 132 ARG cc_start: 0.7129 (mpp80) cc_final: 0.6798 (mpp80) REVERT: G 91 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7082 (mt-10) REVERT: H 9 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.6767 (p90) REVERT: H 25 ASP cc_start: 0.7947 (m-30) cc_final: 0.7684 (p0) REVERT: H 43 LYS cc_start: 0.7146 (tppt) cc_final: 0.6884 (tptp) REVERT: I 168 GLN cc_start: 0.8515 (tp40) cc_final: 0.8091 (mp10) REVERT: J 136 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6388 (ppt170) REVERT: J 225 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6529 (mtp) REVERT: K 48 GLN cc_start: 0.7904 (pt0) cc_final: 0.7657 (pp30) REVERT: L 90 ASN cc_start: 0.8173 (m110) cc_final: 0.7356 (m110) REVERT: L 100 THR cc_start: 0.8033 (t) cc_final: 0.7791 (t) REVERT: L 103 CYS cc_start: 0.7219 (p) cc_final: 0.6687 (p) REVERT: L 111 ASN cc_start: 0.7595 (t0) cc_final: 0.7381 (m-40) outliers start: 77 outliers final: 42 residues processed: 318 average time/residue: 1.3351 time to fit residues: 496.8949 Evaluate side-chains 309 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 255 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 109 CYS Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 2.9990 chunk 267 optimal weight: 0.1980 chunk 163 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 HIS B 505 ASN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN D 126 HIS ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN G 81 HIS H 27 HIS ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN L 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28514 Z= 0.260 Angle : 0.712 16.982 40057 Z= 0.359 Chirality : 0.041 0.217 4792 Planarity : 0.005 0.085 3861 Dihedral : 19.170 175.354 7801 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.84 % Favored : 93.12 % Rotamer: Outliers : 2.66 % Allowed : 25.57 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2485 helix: 0.94 (0.16), residues: 1049 sheet: 0.12 (0.25), residues: 394 loop : -2.13 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP H 118 HIS 0.005 0.001 HIS H 27 PHE 0.014 0.002 PHE D 230 TYR 0.021 0.002 TYR K 18 ARG 0.010 0.001 ARG K 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 267 time to evaluate : 2.568 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: B 107 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6914 (mtm-85) REVERT: B 112 MET cc_start: 0.8583 (mmm) cc_final: 0.8213 (mmt) REVERT: B 145 LYS cc_start: 0.7991 (ptmt) cc_final: 0.7705 (mmtm) REVERT: B 430 MET cc_start: 0.8120 (ttm) cc_final: 0.7831 (ttp) REVERT: B 510 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6955 (tp) REVERT: B 678 ASP cc_start: 0.5921 (OUTLIER) cc_final: 0.5549 (m-30) REVERT: B 714 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6689 (tm-30) REVERT: C 68 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8156 (mm) REVERT: C 140 MET cc_start: 0.5459 (mtm) cc_final: 0.4789 (pmt) REVERT: D 9 LYS cc_start: 0.8352 (tptp) cc_final: 0.7984 (mmmm) REVERT: D 19 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8055 (p0) REVERT: D 72 GLN cc_start: 0.7749 (mp10) cc_final: 0.7523 (tp-100) REVERT: D 219 GLU cc_start: 0.5813 (mp0) cc_final: 0.5439 (mp0) REVERT: D 269 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6601 (ttp-170) REVERT: E 42 ASP cc_start: 0.8397 (t0) cc_final: 0.8062 (t0) REVERT: F 89 GLN cc_start: 0.8084 (tt0) cc_final: 0.7582 (tt0) REVERT: F 131 GLU cc_start: 0.7808 (pt0) cc_final: 0.7522 (pp20) REVERT: F 132 ARG cc_start: 0.7086 (mpp80) cc_final: 0.6663 (mpp80) REVERT: G 91 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7100 (mt-10) REVERT: H 9 TRP cc_start: 0.7584 (OUTLIER) cc_final: 0.6901 (p90) REVERT: H 43 LYS cc_start: 0.7267 (tppt) cc_final: 0.6992 (tptp) REVERT: I 136 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7871 (tmm-80) REVERT: I 168 GLN cc_start: 0.8565 (tp40) cc_final: 0.8203 (mp10) REVERT: J 225 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6692 (mtp) REVERT: K 48 GLN cc_start: 0.7961 (pt0) cc_final: 0.7731 (pp30) REVERT: L 90 ASN cc_start: 0.8197 (m110) cc_final: 0.7356 (m110) REVERT: L 103 CYS cc_start: 0.7440 (p) cc_final: 0.6867 (p) REVERT: L 111 ASN cc_start: 0.7711 (t0) cc_final: 0.7492 (m-40) outliers start: 61 outliers final: 40 residues processed: 309 average time/residue: 1.3113 time to fit residues: 482.5592 Evaluate side-chains 306 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 258 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 109 CYS Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 0.8980 chunk 238 optimal weight: 0.0970 chunk 68 optimal weight: 0.4980 chunk 206 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 HIS B 505 ASN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN D 126 HIS F 37 ASN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 27 HIS ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.147047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.108058 restraints weight = 46597.236| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.39 r_work: 0.3703 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.6808 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: