Starting phenix.real_space_refine on Mon Mar 25 00:43:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr5_27671/03_2024/8dr5_27671_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr5_27671/03_2024/8dr5_27671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr5_27671/03_2024/8dr5_27671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr5_27671/03_2024/8dr5_27671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr5_27671/03_2024/8dr5_27671_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr5_27671/03_2024/8dr5_27671_trim.pdb" } resolution = 2.76 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= 0.043 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 P 63 5.49 5 Mg 4 5.21 5 S 103 5.16 5 C 14224 2.51 5 N 3891 2.21 5 O 4495 1.98 5 H 22595 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F ASP 172": "OD1" <-> "OD2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 156": "OD1" <-> "OD2" Residue "H PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H ASP 204": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45375 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 10233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10233 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 25, 'TRANS': 620} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5084 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 5253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5253 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 5282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5282 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5675 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "F" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4044 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4037 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 4060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4060 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 418 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "J" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 373 Classifications: {'DNA': 12} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 11} Chain: "K" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 363 Classifications: {'DNA': 11} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 10} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 397 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.16, per 1000 atoms: 0.42 Number of scatterers: 45375 At special positions: 0 Unit cell: (149.506, 121.422, 147.028, 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) S 103 16.00 P 63 15.00 Mg 4 11.99 O 4495 8.00 N 3891 7.00 C 14224 6.00 H 22595 1.00 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: 35.65 Conformation dependent library (CDL) restraints added in 4.8 seconds 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5218 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 18 sheets defined 54.7% alpha, 14.2% beta 13 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 20.11 Creating SS restraints... Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.963A pdb=" N TYR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.635A pdb=" N ALA A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 281 removed outlier: 3.634A pdb=" N GLU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 4.021A pdb=" N LYS A 296 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.286A pdb=" N ALA A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.658A pdb=" N ARG A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 560 through 565 removed outlier: 4.187A pdb=" N TYR A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.150A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 714 removed outlier: 4.286A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 removed outlier: 3.657A pdb=" N LEU A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 removed outlier: 4.502A pdb=" N SER A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.967A pdb=" N VAL A 754 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.915A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.607A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 215 removed outlier: 4.205A pdb=" N VAL B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.730A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.531A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 320 Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.600A pdb=" N GLU C 26 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 27' Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.910A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.572A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.731A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.732A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.169A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.917A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.846A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.706A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.741A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 84 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.971A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.554A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.795A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.518A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 334 removed outlier: 3.646A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.570A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.211A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 7.094A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.033A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 226 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.932A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 18 removed outlier: 4.391A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 removed outlier: 3.503A pdb=" N PHE F 57 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 removed outlier: 3.516A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.696A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 3.752A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.435A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 82 removed outlier: 3.585A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.712A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 Processing helix chain 'H' and resid 8 through 18 removed outlier: 4.046A pdb=" N PHE H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 81 removed outlier: 3.942A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 155 removed outlier: 4.236A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.613A pdb=" N THR H 193 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 218 removed outlier: 3.950A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 222 removed outlier: 3.569A pdb=" N SER H 222 " --> pdb=" O SER H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 removed outlier: 6.192A pdb=" N THR A 162 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 200 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 164 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 221 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 377 removed outlier: 8.515A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA A 349 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N CYS A 455 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 351 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 348 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE A 473 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.845A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.288A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.494A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.870A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.646A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.533A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.655A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.138A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 105 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG F 110 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 111 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL H 180 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE H 169 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU H 205 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.085A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY F 34 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE F 245 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.321A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE G 111 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS G 5 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.026A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY G 34 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY G 244 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 180 through 182 removed outlier: 3.538A pdb=" N VAL G 180 " --> pdb=" O PHE G 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 66 through 68 removed outlier: 4.448A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 89 through 91 1184 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 19.35 Time building geometry restraints manager: 36.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 22555 1.05 - 1.27: 3810 1.27 - 1.49: 9068 1.49 - 1.70: 10240 1.70 - 1.92: 162 Bond restraints: 45835 Sorted by residual: bond pdb=" C2' AGS B 402 " pdb=" C3' AGS B 402 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.02e+02 bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.00e+02 bond pdb=" C2' AGS A1002 " pdb=" C3' AGS A1002 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.00e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.94e+02 bond pdb=" C6 AGS A1002 " pdb=" N6 AGS A1002 " ideal model delta sigma weight residual 1.335 1.469 -0.134 1.00e-02 1.00e+04 1.79e+02 ... (remaining 45830 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.34: 504 105.34 - 112.50: 54580 112.50 - 119.67: 11537 119.67 - 126.83: 16256 126.83 - 134.00: 312 Bond angle restraints: 83189 Sorted by residual: angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.03 8.77 8.41e-01 1.41e+00 1.09e+02 angle pdb=" N1 AGS A1002 " pdb=" C2 AGS A1002 " pdb=" N3 AGS A1002 " ideal model delta sigma weight residual 128.80 120.06 8.74 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS C 402 " pdb=" C2 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 128.80 120.11 8.69 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS D 402 " pdb=" C2 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 128.80 120.14 8.66 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS C 402 " pdb=" N7 AGS C 402 " pdb=" C8 AGS C 402 " ideal model delta sigma weight residual 103.67 108.00 -4.33 4.26e-01 5.51e+00 1.03e+02 ... (remaining 83184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 20076 31.31 - 62.62: 990 62.62 - 93.93: 34 93.93 - 125.24: 2 125.24 - 156.54: 4 Dihedral angle restraints: 21106 sinusoidal: 12047 harmonic: 9059 Sorted by residual: dihedral pdb=" O2B GDP E 401 " pdb=" O3A GDP E 401 " pdb=" PB GDP E 401 " pdb=" PA GDP E 401 " ideal model delta sinusoidal sigma weight residual 180.00 23.46 156.54 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" C5' GDP E 401 " pdb=" O5' GDP E 401 " pdb=" PA GDP E 401 " pdb=" O3A GDP E 401 " ideal model delta sinusoidal sigma weight residual 179.98 -67.73 -112.29 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual -67.73 70.44 -138.17 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 21103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3305 0.064 - 0.128: 353 0.128 - 0.192: 16 0.192 - 0.256: 4 0.256 - 0.320: 4 Chirality restraints: 3682 Sorted by residual: chirality pdb=" C2' AGS C 402 " pdb=" C1' AGS C 402 " pdb=" C3' AGS C 402 " pdb=" O2' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.35 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C2' AGS B 402 " pdb=" C1' AGS B 402 " pdb=" C3' AGS B 402 " pdb=" O2' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' AGS A1002 " pdb=" C1' AGS A1002 " pdb=" C3' AGS A1002 " pdb=" O2' AGS A1002 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 3679 not shown) Planarity restraints: 6532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " -0.061 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO E 63 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 131 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO D 132 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 67 " 0.182 9.50e-02 1.11e+02 6.11e-02 4.52e+00 pdb=" NE ARG E 67 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG E 67 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 67 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 67 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 67 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG E 67 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 67 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 67 " 0.000 2.00e-02 2.50e+03 ... (remaining 6529 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1690 2.17 - 2.78: 89251 2.78 - 3.38: 127682 3.38 - 3.99: 168016 3.99 - 4.60: 259987 Nonbonded interactions: 646626 Sorted by model distance: nonbonded pdb=" OE1 GLU F 32 " pdb=" H GLU F 32 " model vdw 1.560 1.850 nonbonded pdb=" OE1 GLN G 24 " pdb=" H GLN G 24 " model vdw 1.603 1.850 nonbonded pdb=" OD1 ASN D 96 " pdb=" HG SER D 98 " model vdw 1.624 1.850 nonbonded pdb=" O LEU D 49 " pdb=" HG1 THR D 52 " model vdw 1.632 1.850 nonbonded pdb=" O ASP H 156 " pdb=" H ALA H 209 " model vdw 1.638 1.850 ... (remaining 646621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and resid 1 through 255) selection = (chain 'G' and resid 1 through 255) selection = (chain 'H' and resid 1 through 255) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.640 Extract box with map and model: 14.030 Check model and map are aligned: 0.610 Set scattering table: 0.360 Process input model: 156.130 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.291 23240 Z= 0.421 Angle : 0.560 8.773 31618 Z= 0.383 Chirality : 0.040 0.320 3682 Planarity : 0.004 0.091 3847 Dihedral : 17.223 156.544 8910 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.82 % Allowed : 16.20 % Favored : 82.98 % 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: 1.42 (0.17), residues: 2729 helix: 1.92 (0.15), residues: 1304 sheet: 0.08 (0.22), residues: 516 loop : 0.15 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 27 HIS 0.006 0.001 HIS A 610 PHE 0.011 0.001 PHE F 245 TYR 0.006 0.001 TYR D 286 ARG 0.012 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 358 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 MET cc_start: 0.6920 (pp-130) cc_final: 0.6206 (ppp) outliers start: 20 outliers final: 9 residues processed: 372 average time/residue: 3.4984 time to fit residues: 1469.5138 Evaluate side-chains 195 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.5980 chunk 208 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 326 ASN A 368 GLN A 546 ASN A 571 ASN B 204 GLN C 202 ASN C 264 ASN C 319 GLN D 236 GLN D 250 ASN E 224 GLN F 29 GLN G 83 ASN G 84 ASN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23240 Z= 0.189 Angle : 0.524 6.837 31618 Z= 0.279 Chirality : 0.039 0.151 3682 Planarity : 0.004 0.056 3847 Dihedral : 13.593 160.256 3522 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.60 % Allowed : 18.96 % Favored : 78.44 % 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: 1.45 (0.17), residues: 2729 helix: 1.99 (0.15), residues: 1302 sheet: 0.19 (0.22), residues: 506 loop : 0.02 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.006 0.001 HIS A 418 PHE 0.011 0.001 PHE G 185 TYR 0.009 0.001 TYR H 114 ARG 0.009 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 194 time to evaluate : 3.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 MET cc_start: 0.6957 (pp-130) cc_final: 0.6255 (ppp) outliers start: 63 outliers final: 17 residues processed: 240 average time/residue: 3.0985 time to fit residues: 847.3944 Evaluate side-chains 194 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 162 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 170 optimal weight: 0.0570 chunk 68 optimal weight: 0.5980 chunk 250 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN A 546 ASN B 220 ASN G 83 ASN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23240 Z= 0.203 Angle : 0.498 6.200 31618 Z= 0.266 Chirality : 0.039 0.157 3682 Planarity : 0.004 0.067 3847 Dihedral : 13.421 165.677 3517 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.02 % Allowed : 19.08 % Favored : 78.90 % 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: 1.49 (0.17), residues: 2729 helix: 2.07 (0.15), residues: 1298 sheet: 0.24 (0.22), residues: 513 loop : -0.05 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.012 0.001 HIS A 337 PHE 0.012 0.001 PHE E 328 TYR 0.017 0.001 TYR H 114 ARG 0.012 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 183 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7486 (mpp) REVERT: H 1 MET cc_start: 0.2579 (pp-130) cc_final: 0.2335 (pmt) REVERT: H 70 MET cc_start: 0.6991 (pp-130) cc_final: 0.6208 (ppp) outliers start: 49 outliers final: 23 residues processed: 218 average time/residue: 3.0378 time to fit residues: 758.5080 Evaluate side-chains 192 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 199 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23240 Z= 0.267 Angle : 0.509 6.002 31618 Z= 0.274 Chirality : 0.040 0.176 3682 Planarity : 0.004 0.049 3847 Dihedral : 13.485 166.993 3513 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.69 % Allowed : 19.58 % Favored : 78.73 % 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: 1.45 (0.17), residues: 2729 helix: 2.03 (0.15), residues: 1286 sheet: 0.22 (0.22), residues: 523 loop : -0.02 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.006 0.001 HIS A 610 PHE 0.016 0.001 PHE G 185 TYR 0.013 0.001 TYR H 133 ARG 0.006 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7528 (mpp) REVERT: H 1 MET cc_start: 0.2644 (pp-130) cc_final: 0.2427 (pmt) REVERT: H 70 MET cc_start: 0.7051 (pp-130) cc_final: 0.6560 (ppp) outliers start: 41 outliers final: 25 residues processed: 199 average time/residue: 3.1434 time to fit residues: 722.5197 Evaluate side-chains 188 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN B 317 HIS E 110 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 23240 Z= 0.439 Angle : 0.577 6.328 31618 Z= 0.311 Chirality : 0.043 0.174 3682 Planarity : 0.004 0.056 3847 Dihedral : 13.768 179.807 3513 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.10 % Allowed : 18.76 % Favored : 79.14 % 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: 0.93 (0.16), residues: 2729 helix: 1.54 (0.15), residues: 1302 sheet: 0.21 (0.22), residues: 514 loop : -0.38 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.009 0.002 HIS B 44 PHE 0.020 0.002 PHE E 328 TYR 0.018 0.002 TYR D 286 ARG 0.025 0.001 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 163 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 488 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7621 (mpp) REVERT: B 226 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8520 (mtpp) REVERT: H 1 MET cc_start: 0.2619 (pp-130) cc_final: 0.2403 (pmt) REVERT: H 70 MET cc_start: 0.7147 (pp-130) cc_final: 0.6570 (ppp) outliers start: 51 outliers final: 24 residues processed: 202 average time/residue: 3.3765 time to fit residues: 772.0589 Evaluate side-chains 184 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 174 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 GLN F 58 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23240 Z= 0.195 Angle : 0.509 6.447 31618 Z= 0.274 Chirality : 0.039 0.166 3682 Planarity : 0.004 0.043 3847 Dihedral : 13.637 170.973 3513 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 19.50 % Favored : 79.02 % 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: 1.18 (0.16), residues: 2729 helix: 1.78 (0.15), residues: 1305 sheet: 0.15 (0.22), residues: 528 loop : -0.20 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS E 18 PHE 0.016 0.001 PHE G 185 TYR 0.017 0.001 TYR H 133 ARG 0.007 0.000 ARG G 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7626 (mmtp) REVERT: A 470 CYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7747 (m) REVERT: H 70 MET cc_start: 0.7132 (pp-130) cc_final: 0.6555 (ppp) outliers start: 36 outliers final: 22 residues processed: 192 average time/residue: 3.2676 time to fit residues: 712.5638 Evaluate side-chains 179 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 188 MET Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 199 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 58 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23240 Z= 0.292 Angle : 0.524 8.081 31618 Z= 0.281 Chirality : 0.040 0.161 3682 Planarity : 0.004 0.046 3847 Dihedral : 13.600 168.660 3513 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.61 % Allowed : 19.08 % Favored : 79.31 % 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: 1.13 (0.16), residues: 2729 helix: 1.75 (0.15), residues: 1304 sheet: 0.13 (0.22), residues: 528 loop : -0.26 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.006 0.001 HIS A 610 PHE 0.015 0.001 PHE E 328 TYR 0.019 0.001 TYR H 133 ARG 0.010 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7797 (m) REVERT: C 43 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: H 70 MET cc_start: 0.7148 (pp-130) cc_final: 0.6561 (ppp) outliers start: 39 outliers final: 21 residues processed: 186 average time/residue: 3.3493 time to fit residues: 714.0680 Evaluate side-chains 177 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 188 MET Chi-restraints excluded: chain H residue 162 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 180 optimal weight: 0.0270 chunk 131 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23240 Z= 0.187 Angle : 0.504 8.698 31618 Z= 0.269 Chirality : 0.039 0.162 3682 Planarity : 0.004 0.108 3847 Dihedral : 13.496 166.509 3513 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.99 % Allowed : 19.54 % Favored : 79.47 % 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: 1.27 (0.17), residues: 2729 helix: 1.87 (0.15), residues: 1308 sheet: 0.16 (0.22), residues: 528 loop : -0.18 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.004 0.001 HIS D 124 PHE 0.022 0.001 PHE G 185 TYR 0.021 0.001 TYR H 133 ARG 0.020 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7793 (m) REVERT: G 190 HIS cc_start: 0.6843 (p-80) cc_final: 0.6398 (p90) REVERT: H 70 MET cc_start: 0.7135 (pp-130) cc_final: 0.6548 (ppp) outliers start: 24 outliers final: 19 residues processed: 179 average time/residue: 3.2823 time to fit residues: 667.1830 Evaluate side-chains 172 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain H residue 162 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 GLN G 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23240 Z= 0.265 Angle : 0.540 15.860 31618 Z= 0.289 Chirality : 0.040 0.322 3682 Planarity : 0.004 0.098 3847 Dihedral : 13.502 167.671 3512 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.24 % Allowed : 19.54 % Favored : 79.23 % 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: 1.23 (0.16), residues: 2729 helix: 1.85 (0.15), residues: 1301 sheet: 0.26 (0.23), residues: 499 loop : -0.28 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS B 317 PHE 0.105 0.001 PHE G 185 TYR 0.020 0.001 TYR H 133 ARG 0.021 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7813 (m) REVERT: H 70 MET cc_start: 0.7143 (pp-130) cc_final: 0.6552 (ppp) outliers start: 30 outliers final: 22 residues processed: 177 average time/residue: 3.1704 time to fit residues: 641.0419 Evaluate side-chains 174 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 162 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 173 optimal weight: 0.0670 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23240 Z= 0.243 Angle : 0.527 8.520 31618 Z= 0.280 Chirality : 0.039 0.167 3682 Planarity : 0.004 0.085 3847 Dihedral : 13.454 167.563 3512 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.15 % Allowed : 19.70 % Favored : 79.14 % 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: 1.23 (0.16), residues: 2729 helix: 1.85 (0.15), residues: 1301 sheet: 0.25 (0.23), residues: 501 loop : -0.27 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS E 18 PHE 0.013 0.001 PHE E 328 TYR 0.023 0.001 TYR H 133 ARG 0.017 0.001 ARG A 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 CYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7871 (m) REVERT: G 190 HIS cc_start: 0.6593 (p-80) cc_final: 0.6363 (p-80) REVERT: H 70 MET cc_start: 0.7171 (pp-130) cc_final: 0.6577 (ppp) outliers start: 28 outliers final: 23 residues processed: 177 average time/residue: 3.4381 time to fit residues: 703.8228 Evaluate side-chains 177 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 162 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 201 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 27 optimal weight: 0.0670 chunk 40 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 ASN G 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.108151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072766 restraints weight = 116911.064| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.40 r_work: 0.2999 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23240 Z= 0.171 Angle : 0.508 8.526 31618 Z= 0.269 Chirality : 0.038 0.166 3682 Planarity : 0.004 0.095 3847 Dihedral : 13.383 166.248 3512 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.11 % Allowed : 19.74 % Favored : 79.14 % 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: 1.38 (0.17), residues: 2729 helix: 1.98 (0.15), residues: 1301 sheet: 0.27 (0.23), residues: 501 loop : -0.16 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.004 0.001 HIS D 124 PHE 0.011 0.001 PHE E 328 TYR 0.024 0.001 TYR H 114 ARG 0.016 0.000 ARG A 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14767.75 seconds wall clock time: 258 minutes 25.08 seconds (15505.08 seconds total)