Starting phenix.real_space_refine on Sat Dec 9 02:15:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c76_30293/12_2023/7c76_30293.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c76_30293/12_2023/7c76_30293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c76_30293/12_2023/7c76_30293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c76_30293/12_2023/7c76_30293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c76_30293/12_2023/7c76_30293.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c76_30293/12_2023/7c76_30293.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6318 2.51 5 N 1600 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ASP 641": "OD1" <-> "OD2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 692": "OD1" <-> "OD2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 374": "NH1" <-> "NH2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B ARG 520": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9762 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5563 Classifications: {'peptide': 691} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3855 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 20, 'TRANS': 462} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.59 Number of scatterers: 9762 At special positions: 0 Unit cell: (135.705, 176.79, 94.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1804 8.00 N 1600 7.00 C 6318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.04 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 651 " - pdb=" SG CYS A 696 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 368 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1001 " - " ASN A 52 " " NAG A1002 " - " ASN A 57 " " NAG A1003 " - " ASN A 70 " " NAG A1004 " - " ASN A 124 " " NAG A1005 " - " ASN A 196 " " NAG A1013 " - " ASN A 265 " " NAG A1014 " - " ASN A 291 " " NAG A1022 " - " ASN A 662 " " NAG B 601 " - " ASN B 251 " " NAG C 1 " - " ASN A 247 " " NAG D 1 " - " ASN A 252 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 413 " " NAG G 1 " - " ASN A 398 " " NAG H 1 " - " ASN A 507 " " NAG I 1 " - " ASN B 272 " Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 42.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.592A pdb=" N THR A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.298A pdb=" N CYS A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.615A pdb=" N THR A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 120 " --> pdb=" O LYS A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 120' Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.568A pdb=" N LEU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.641A pdb=" N ILE A 220 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.681A pdb=" N LYS A 272 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 632 through 635 removed outlier: 3.685A pdb=" N ARG A 635 " --> pdb=" O PRO A 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 632 through 635' Processing helix chain 'A' and resid 650 through 663 removed outlier: 6.301A pdb=" N TRP A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 701 through 726 Processing helix chain 'B' and resid 46 through 89 Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 117 through 123 removed outlier: 4.350A pdb=" N ALA B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 123 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 136 through 152 Processing helix chain 'B' and resid 157 through 199 Proline residue: B 163 - end of helix removed outlier: 4.582A pdb=" N VAL B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 213 through 235 removed outlier: 3.935A pdb=" N VAL B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.992A pdb=" N THR B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 removed outlier: 3.554A pdb=" N SER B 264 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 306 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.546A pdb=" N GLU B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.903A pdb=" N ILE B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE B 328 " --> pdb=" O TRP B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 323 through 328' Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 339 through 359 Proline residue: B 345 - end of helix Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.429A pdb=" N SER B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 374 through 396 removed outlier: 3.633A pdb=" N LEU B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 422 removed outlier: 4.297A pdb=" N LEU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 461 removed outlier: 3.881A pdb=" N TYR B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 488 Processing helix chain 'B' and resid 494 through 518 removed outlier: 3.766A pdb=" N LEU B 518 " --> pdb=" O MET B 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.243A pdb=" N ALA A 35 " --> pdb=" O ASN A 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.869A pdb=" N LEU A 128 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA6, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.914A pdb=" N LEU A 226 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 253 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 279 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 327 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE A 461 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA9, first strand: chain 'A' and resid 395 through 396 Processing sheet with id=AB1, first strand: chain 'A' and resid 444 through 446 Processing sheet with id=AB2, first strand: chain 'A' and resid 614 through 616 349 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3031 1.35 - 1.46: 2472 1.46 - 1.58: 4424 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 9992 Sorted by residual: bond pdb=" C PRO B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 4.14e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 9987 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.46: 365 107.46 - 114.11: 5836 114.11 - 120.75: 4062 120.75 - 127.40: 3198 127.40 - 134.05: 112 Bond angle restraints: 13573 Sorted by residual: angle pdb=" C ASN A 140 " pdb=" N ASN A 141 " pdb=" CA ASN A 141 " ideal model delta sigma weight residual 121.80 129.06 -7.26 2.44e+00 1.68e-01 8.86e+00 angle pdb=" N ASN A 141 " pdb=" CA ASN A 141 " pdb=" C ASN A 141 " ideal model delta sigma weight residual 109.81 115.24 -5.43 2.21e+00 2.05e-01 6.03e+00 angle pdb=" CA LEU B 500 " pdb=" CB LEU B 500 " pdb=" CG LEU B 500 " ideal model delta sigma weight residual 116.30 124.18 -7.88 3.50e+00 8.16e-02 5.07e+00 angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" C PRO B 208 " ideal model delta sigma weight residual 110.70 113.31 -2.61 1.22e+00 6.72e-01 4.59e+00 angle pdb=" N THR B 126 " pdb=" CA THR B 126 " pdb=" C THR B 126 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.50e+00 ... (remaining 13568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5413 17.93 - 35.85: 626 35.85 - 53.78: 133 53.78 - 71.70: 23 71.70 - 89.63: 10 Dihedral angle restraints: 6205 sinusoidal: 2769 harmonic: 3436 Sorted by residual: dihedral pdb=" CA PRO B 208 " pdb=" C PRO B 208 " pdb=" N PRO B 209 " pdb=" CA PRO B 209 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS A 95 " pdb=" SG CYS A 95 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -48.50 -37.50 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CB CYS B 260 " pdb=" SG CYS B 260 " pdb=" SG CYS B 368 " pdb=" CB CYS B 368 " ideal model delta sinusoidal sigma weight residual 93.00 121.39 -28.39 1 1.00e+01 1.00e-02 1.15e+01 ... (remaining 6202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1395 0.058 - 0.116: 212 0.116 - 0.174: 12 0.174 - 0.232: 1 0.232 - 0.290: 3 Chirality restraints: 1623 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 247 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1620 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 312 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 313 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 207 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 208 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 208 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 209 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " 0.024 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1208 2.76 - 3.29: 9743 3.29 - 3.83: 16679 3.83 - 4.36: 18951 4.36 - 4.90: 32613 Nonbonded interactions: 79194 Sorted by model distance: nonbonded pdb=" O HIS B 229 " pdb=" OG SER B 383 " model vdw 2.219 2.440 nonbonded pdb=" O ASP A 347 " pdb=" OG SER A 350 " model vdw 2.267 2.440 nonbonded pdb=" O LEU A 637 " pdb=" OG1 THR A 666 " model vdw 2.272 2.440 nonbonded pdb=" O THR B 135 " pdb=" OG SER B 178 " model vdw 2.277 2.440 nonbonded pdb=" OE1 GLU B 353 " pdb=" OG SER B 446 " model vdw 2.278 2.440 ... (remaining 79189 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 'C' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.310 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.270 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.003 0.034 9992 Z= 0.215 Angle : 0.629 7.878 13573 Z= 0.305 Chirality : 0.043 0.290 1623 Planarity : 0.003 0.048 1672 Dihedral : 15.648 89.628 3973 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 1.91 % Allowed : 10.22 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.76 (0.23), residues: 1168 helix: -0.53 (0.24), residues: 418 sheet: -3.24 (0.43), residues: 120 loop : -2.51 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 476 HIS 0.009 0.000 HIS B 475 PHE 0.013 0.001 PHE A 647 TYR 0.011 0.001 TYR B 248 ARG 0.007 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 318 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 332 average time/residue: 0.1955 time to fit residues: 93.4504 Evaluate side-chains 279 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 272 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1032 time to fit residues: 2.8206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN A 410 HIS A 539 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 9992 Z= 0.499 Angle : 0.784 9.705 13573 Z= 0.384 Chirality : 0.049 0.329 1623 Planarity : 0.005 0.046 1672 Dihedral : 5.922 54.443 1743 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 3.25 % Allowed : 20.92 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.71 (0.25), residues: 1168 helix: 0.46 (0.26), residues: 422 sheet: -3.22 (0.46), residues: 110 loop : -1.91 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 656 HIS 0.010 0.001 HIS A 724 PHE 0.026 0.002 PHE A 702 TYR 0.023 0.002 TYR B 90 ARG 0.005 0.001 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 279 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 25 residues processed: 294 average time/residue: 0.1816 time to fit residues: 79.0247 Evaluate side-chains 287 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 262 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0976 time to fit residues: 5.9361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN A 539 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 334 HIS ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9992 Z= 0.191 Angle : 0.629 11.101 13573 Z= 0.295 Chirality : 0.044 0.249 1623 Planarity : 0.004 0.049 1672 Dihedral : 5.531 52.686 1743 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 2.20 % Allowed : 22.45 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.20 (0.25), residues: 1168 helix: 0.94 (0.27), residues: 429 sheet: -3.05 (0.48), residues: 110 loop : -1.65 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 476 HIS 0.008 0.001 HIS B 475 PHE 0.016 0.001 PHE A 706 TYR 0.019 0.001 TYR B 511 ARG 0.008 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 279 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 291 average time/residue: 0.1932 time to fit residues: 82.7983 Evaluate side-chains 274 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 262 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0979 time to fit residues: 3.7207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9992 Z= 0.307 Angle : 0.660 7.832 13573 Z= 0.321 Chirality : 0.046 0.288 1623 Planarity : 0.004 0.065 1672 Dihedral : 5.642 54.607 1743 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 4.11 % Allowed : 24.07 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.97 (0.26), residues: 1168 helix: 1.25 (0.27), residues: 407 sheet: -2.95 (0.50), residues: 110 loop : -1.51 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 476 HIS 0.007 0.001 HIS B 412 PHE 0.021 0.002 PHE A 630 TYR 0.020 0.002 TYR B 90 ARG 0.004 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 261 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 286 average time/residue: 0.1726 time to fit residues: 73.8647 Evaluate side-chains 270 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1100 time to fit residues: 5.7977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.0050 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN B 244 ASN ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9992 Z= 0.171 Angle : 0.627 11.460 13573 Z= 0.293 Chirality : 0.043 0.247 1623 Planarity : 0.004 0.053 1672 Dihedral : 5.402 53.946 1743 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 1.53 % Allowed : 27.13 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.76 (0.26), residues: 1168 helix: 1.38 (0.27), residues: 410 sheet: -2.83 (0.48), residues: 119 loop : -1.33 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 137 HIS 0.007 0.001 HIS B 475 PHE 0.020 0.001 PHE B 483 TYR 0.016 0.001 TYR B 349 ARG 0.005 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 272 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 281 average time/residue: 0.1809 time to fit residues: 75.5699 Evaluate side-chains 254 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 248 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1535 time to fit residues: 2.9527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9992 Z= 0.181 Angle : 0.618 7.534 13573 Z= 0.292 Chirality : 0.044 0.249 1623 Planarity : 0.004 0.053 1672 Dihedral : 5.192 52.423 1743 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 2.29 % Allowed : 28.94 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.71 (0.26), residues: 1168 helix: 1.43 (0.27), residues: 410 sheet: -2.78 (0.48), residues: 119 loop : -1.30 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 137 HIS 0.007 0.001 HIS B 475 PHE 0.019 0.001 PHE B 483 TYR 0.020 0.001 TYR B 349 ARG 0.002 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 269 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 277 average time/residue: 0.1761 time to fit residues: 72.6976 Evaluate side-chains 272 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 259 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0903 time to fit residues: 3.5100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.0010 chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9992 Z= 0.175 Angle : 0.616 8.570 13573 Z= 0.291 Chirality : 0.043 0.247 1623 Planarity : 0.004 0.050 1672 Dihedral : 5.020 52.474 1743 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 1.34 % Allowed : 28.94 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.63 (0.26), residues: 1168 helix: 1.43 (0.27), residues: 410 sheet: -2.73 (0.48), residues: 119 loop : -1.21 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 137 HIS 0.006 0.001 HIS B 475 PHE 0.019 0.001 PHE B 346 TYR 0.017 0.001 TYR A 383 ARG 0.004 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 275 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 279 average time/residue: 0.1855 time to fit residues: 76.5963 Evaluate side-chains 265 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0992 time to fit residues: 2.6158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS A 607 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9992 Z= 0.302 Angle : 0.705 13.049 13573 Z= 0.330 Chirality : 0.046 0.277 1623 Planarity : 0.004 0.044 1672 Dihedral : 5.306 53.182 1743 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 1.24 % Allowed : 30.18 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.64 (0.26), residues: 1168 helix: 1.52 (0.27), residues: 404 sheet: -2.73 (0.51), residues: 109 loop : -1.31 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 476 HIS 0.006 0.001 HIS A 724 PHE 0.027 0.002 PHE B 346 TYR 0.019 0.002 TYR B 90 ARG 0.003 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 266 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 273 average time/residue: 0.1926 time to fit residues: 76.9155 Evaluate side-chains 263 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 256 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1052 time to fit residues: 2.7831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9992 Z= 0.196 Angle : 0.685 12.326 13573 Z= 0.312 Chirality : 0.045 0.248 1623 Planarity : 0.004 0.044 1672 Dihedral : 5.186 52.607 1743 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 0.76 % Allowed : 31.14 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.57 (0.26), residues: 1168 helix: 1.45 (0.27), residues: 411 sheet: -2.68 (0.48), residues: 119 loop : -1.16 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 476 HIS 0.006 0.001 HIS B 475 PHE 0.018 0.001 PHE B 346 TYR 0.017 0.001 TYR A 383 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 263 average time/residue: 0.1896 time to fit residues: 73.8790 Evaluate side-chains 255 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 251 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1009 time to fit residues: 2.3048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9992 Z= 0.203 Angle : 0.690 10.453 13573 Z= 0.313 Chirality : 0.045 0.257 1623 Planarity : 0.004 0.043 1672 Dihedral : 5.052 52.935 1743 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 0.38 % Allowed : 31.90 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.55 (0.26), residues: 1168 helix: 1.43 (0.27), residues: 411 sheet: -2.61 (0.48), residues: 118 loop : -1.13 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 477 HIS 0.006 0.001 HIS B 475 PHE 0.017 0.001 PHE B 346 TYR 0.017 0.001 TYR A 383 ARG 0.003 0.000 ARG B 519 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 258 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 260 average time/residue: 0.1892 time to fit residues: 72.0401 Evaluate side-chains 256 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0879 time to fit residues: 1.7273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.161493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132026 restraints weight = 16145.047| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.48 r_work: 0.3637 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9992 Z= 0.190 Angle : 0.696 11.166 13573 Z= 0.318 Chirality : 0.045 0.244 1623 Planarity : 0.004 0.043 1672 Dihedral : 4.904 52.397 1743 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 0.48 % Allowed : 32.28 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.49 (0.26), residues: 1168 helix: 1.50 (0.27), residues: 406 sheet: -2.59 (0.48), residues: 118 loop : -1.09 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 477 HIS 0.006 0.001 HIS B 412 PHE 0.015 0.001 PHE A 706 TYR 0.063 0.002 TYR B 349 ARG 0.006 0.000 ARG B 519 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.37 seconds wall clock time: 44 minutes 47.99 seconds (2687.99 seconds total)