Starting phenix.real_space_refine on Sat Dec 9 20:24:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri4_24473/12_2023/7ri4_24473.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri4_24473/12_2023/7ri4_24473.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/7ri4_24473/12_2023/7ri4_24473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri4_24473/12_2023/7ri4_24473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri4_24473/12_2023/7ri4_24473.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ri4_24473/12_2023/7ri4_24473.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= 0.005 sd= 0.077 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 36 5.16 5 C 7713 2.51 5 N 2097 2.21 5 O 2402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 1270": "OD1" <-> "OD2" Residue "G PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1277": "OE1" <-> "OE2" Residue "G PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1297": "NH1" <-> "NH2" Residue "G TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 28": "OD1" <-> "OD2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 493": "OD1" <-> "OD2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 589": "OD1" <-> "OD2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 639": "OD1" <-> "OD2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 687": "OD1" <-> "OD2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A ASP 698": "OD1" <-> "OD2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 727": "OD1" <-> "OD2" Residue "A PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 762": "OD1" <-> "OD2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 795": "OD1" <-> "OD2" Residue "A ASP 797": "OD1" <-> "OD2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ASP 248": "OD1" <-> "OD2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 131": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 105": "OD1" <-> "OD2" 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: 12248 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 434 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain breaks: 1 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: 3 Chain: "A" Number of atoms: 6189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6189 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 752} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2733 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 437 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1760 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 207} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 6.72, per 1000 atoms: 0.55 Number of scatterers: 12248 At special positions: 0 Unit cell: (108, 143.64, 127.44, 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 36 16.00 O 2402 8.00 N 2097 7.00 C 7713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G1226 " - pdb=" SG CYS A 806 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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 Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 2.4 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2886 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 19.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.702A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.882A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 4.159A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 removed outlier: 4.019A pdb=" N PHE A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.061A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.811A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.516A pdb=" N LYS A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.526A pdb=" N VAL A 364 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.994A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.562A pdb=" N GLU A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 651' Processing helix chain 'A' and resid 655 through 660 removed outlier: 3.772A pdb=" N THR A 659 " --> pdb=" O GLY A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.717A pdb=" N ALA A 730 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.595A pdb=" N ARG B 243 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 244 " --> pdb=" O ILE B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 244' Processing helix chain 'D' and resid 33 through 44 removed outlier: 3.894A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 39 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 4.377A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 68 through 82 removed outlier: 4.064A pdb=" N GLN D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 99 removed outlier: 3.803A pdb=" N ASN D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 119 removed outlier: 3.562A pdb=" N MET D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 154 removed outlier: 3.883A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 removed outlier: 3.668A pdb=" N THR D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.618A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 214 through 223 removed outlier: 4.020A pdb=" N ASN D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 4.011A pdb=" N GLU D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.574A pdb=" N LYS E 45 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.520A pdb=" N TYR E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.323A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.846A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 156 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 removed outlier: 6.836A pdb=" N GLU A 176 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N VAL A 256 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 247 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 270 removed outlier: 7.374A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.901A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 430 Processing sheet with id=AA8, first strand: chain 'A' and resid 461 through 462 removed outlier: 4.284A pdb=" N TYR A 468 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 485 through 492 removed outlier: 3.985A pdb=" N ALA A 527 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 576 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG A 592 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 594 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 564 through 569 removed outlier: 3.580A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 576 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG A 592 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 594 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 49 removed outlier: 7.007A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.549A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 118 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AB6, first strand: chain 'B' and resid 287 through 290 removed outlier: 3.596A pdb=" N ASN B 287 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 299 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE B 289 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR B 297 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.736A pdb=" N ARG E 78 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.736A pdb=" N ARG E 78 " --> pdb=" O GLN E 34 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 876 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: 3.59 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4106 1.34 - 1.46: 2821 1.46 - 1.58: 5514 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 12509 Sorted by residual: bond pdb=" C PRO D 31 " pdb=" N PRO D 32 " ideal model delta sigma weight residual 1.326 1.366 -0.040 1.44e-02 4.82e+03 7.69e+00 bond pdb=" CA GLY C 77 " pdb=" C GLY C 77 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.47e+00 bond pdb=" C LEU D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.24e+00 bond pdb=" N GLY C 77 " pdb=" CA GLY C 77 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.76e+00 bond pdb=" C ILE C 67 " pdb=" N PRO C 68 " ideal model delta sigma weight residual 1.331 1.347 -0.015 1.21e-02 6.83e+03 1.61e+00 ... (remaining 12504 not shown) Histogram of bond angle deviations from ideal: 100.65 - 107.33: 408 107.33 - 114.01: 6726 114.01 - 120.69: 4899 120.69 - 127.37: 4864 127.37 - 134.05: 106 Bond angle restraints: 17003 Sorted by residual: angle pdb=" N TYR A 548 " pdb=" CA TYR A 548 " pdb=" C TYR A 548 " ideal model delta sigma weight residual 113.18 107.37 5.81 1.33e+00 5.65e-01 1.91e+01 angle pdb=" N ILE B 92 " pdb=" CA ILE B 92 " pdb=" C ILE B 92 " ideal model delta sigma weight residual 112.12 108.49 3.63 8.40e-01 1.42e+00 1.86e+01 angle pdb=" N ASP B 384 " pdb=" CA ASP B 384 " pdb=" C ASP B 384 " ideal model delta sigma weight residual 114.56 109.15 5.41 1.27e+00 6.20e-01 1.81e+01 angle pdb=" N ASN G1290 " pdb=" CA ASN G1290 " pdb=" C ASN G1290 " ideal model delta sigma weight residual 108.23 113.96 -5.73 1.38e+00 5.25e-01 1.72e+01 angle pdb=" CA LEU G1259 " pdb=" CB LEU G1259 " pdb=" CG LEU G1259 " ideal model delta sigma weight residual 116.30 130.52 -14.22 3.50e+00 8.16e-02 1.65e+01 ... (remaining 16998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6359 17.97 - 35.95: 794 35.95 - 53.92: 187 53.92 - 71.90: 29 71.90 - 89.87: 20 Dihedral angle restraints: 7389 sinusoidal: 2855 harmonic: 4534 Sorted by residual: dihedral pdb=" CA ASN D 30 " pdb=" C ASN D 30 " pdb=" N PRO D 31 " pdb=" CA PRO D 31 " ideal model delta harmonic sigma weight residual 180.00 140.15 39.85 0 5.00e+00 4.00e-02 6.35e+01 dihedral pdb=" CA PRO D 31 " pdb=" C PRO D 31 " pdb=" N PRO D 32 " pdb=" CA PRO D 32 " ideal model delta harmonic sigma weight residual -180.00 -141.46 -38.54 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" CA ASP G1289 " pdb=" C ASP G1289 " pdb=" N ASN G1290 " pdb=" CA ASN G1290 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1378 0.044 - 0.088: 370 0.088 - 0.132: 108 0.132 - 0.176: 4 0.176 - 0.220: 2 Chirality restraints: 1862 Sorted by residual: chirality pdb=" CG LEU G1259 " pdb=" CB LEU G1259 " pdb=" CD1 LEU G1259 " pdb=" CD2 LEU G1259 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO D 86 " pdb=" N PRO D 86 " pdb=" C PRO D 86 " pdb=" CB PRO D 86 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA PRO A 602 " pdb=" N PRO A 602 " pdb=" C PRO A 602 " pdb=" CB PRO A 602 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1859 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 30 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO D 31 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 675 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 676 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 540 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO A 541 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " -0.023 5.00e-02 4.00e+02 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2132 2.77 - 3.30: 11579 3.30 - 3.84: 18768 3.84 - 4.37: 21159 4.37 - 4.90: 37273 Nonbonded interactions: 90911 Sorted by model distance: nonbonded pdb=" OH TYR D 36 " pdb=" OE1 GLN D 70 " model vdw 2.238 2.440 nonbonded pdb=" ND2 ASN A 102 " pdb=" O VAL A 105 " model vdw 2.250 2.520 nonbonded pdb=" N ALA B 260 " pdb=" OG1 THR B 268 " model vdw 2.266 2.520 nonbonded pdb=" OE2 GLU A 305 " pdb=" OG SER A 324 " model vdw 2.311 2.440 nonbonded pdb=" O ARG A 350 " pdb=" NE ARG A 350 " model vdw 2.329 2.520 ... (remaining 90906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 4.330 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 33.920 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 0.055 12509 Z= 0.182 Angle : 0.745 14.221 17003 Z= 0.437 Chirality : 0.043 0.220 1862 Planarity : 0.004 0.103 2242 Dihedral : 17.059 89.870 4497 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.85 % Favored : 85.96 % Rotamer: Outliers : 3.70 % Allowed : 13.26 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % 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: -5.39 (0.16), residues: 1560 helix: -3.14 (0.22), residues: 266 sheet: -3.08 (0.25), residues: 342 loop : -4.12 (0.15), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 93 HIS 0.003 0.001 HIS B 347 PHE 0.014 0.001 PHE D 64 TYR 0.016 0.001 TYR A 522 ARG 0.006 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 1.418 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 29 residues processed: 268 average time/residue: 0.2188 time to fit residues: 86.7316 Evaluate side-chains 203 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1449 time to fit residues: 8.8801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 121 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 52 GLN E 83 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12509 Z= 0.316 Angle : 0.748 10.393 17003 Z= 0.393 Chirality : 0.047 0.216 1862 Planarity : 0.005 0.102 2242 Dihedral : 6.047 43.430 1725 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.41 % Favored : 83.40 % Rotamer: Outliers : 5.24 % Allowed : 20.59 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % 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: -4.80 (0.18), residues: 1560 helix: -1.92 (0.27), residues: 288 sheet: -2.98 (0.24), residues: 381 loop : -3.88 (0.16), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 745 HIS 0.007 0.001 HIS A 677 PHE 0.016 0.002 PHE A 565 TYR 0.019 0.002 TYR A 760 ARG 0.008 0.001 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 170 time to evaluate : 1.685 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 37 residues processed: 219 average time/residue: 0.2144 time to fit residues: 70.2922 Evaluate side-chains 194 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 1.431 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1150 time to fit residues: 9.6469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 52 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12509 Z= 0.168 Angle : 0.645 8.986 17003 Z= 0.335 Chirality : 0.044 0.200 1862 Planarity : 0.005 0.102 2242 Dihedral : 5.633 39.420 1725 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.13 % Favored : 84.74 % Rotamer: Outliers : 2.78 % Allowed : 25.13 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % 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: -4.31 (0.19), residues: 1560 helix: -1.14 (0.30), residues: 285 sheet: -2.64 (0.26), residues: 357 loop : -3.72 (0.16), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 93 HIS 0.003 0.001 HIS A 677 PHE 0.022 0.001 PHE G1278 TYR 0.014 0.001 TYR B 333 ARG 0.004 0.000 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 1.490 Fit side-chains outliers start: 36 outliers final: 21 residues processed: 206 average time/residue: 0.2249 time to fit residues: 69.1780 Evaluate side-chains 181 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1295 time to fit residues: 7.1065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.0050 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN E 34 GLN E 52 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 0.063 12509 Z= 0.189 Angle : 0.646 8.532 17003 Z= 0.338 Chirality : 0.044 0.297 1862 Planarity : 0.005 0.099 2242 Dihedral : 5.652 39.837 1725 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.71 % Favored : 84.17 % Rotamer: Outliers : 3.93 % Allowed : 25.98 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % 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: -4.05 (0.19), residues: 1560 helix: -0.75 (0.30), residues: 289 sheet: -2.55 (0.26), residues: 360 loop : -3.58 (0.17), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 93 HIS 0.003 0.001 HIS A 677 PHE 0.018 0.001 PHE A 197 TYR 0.036 0.001 TYR D 107 ARG 0.006 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 164 time to evaluate : 1.470 Fit side-chains outliers start: 51 outliers final: 27 residues processed: 197 average time/residue: 0.2291 time to fit residues: 67.4874 Evaluate side-chains 178 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1188 time to fit residues: 7.7956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.0570 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 52 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12509 Z= 0.205 Angle : 0.655 8.722 17003 Z= 0.342 Chirality : 0.044 0.207 1862 Planarity : 0.005 0.095 2242 Dihedral : 5.697 40.242 1725 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.77 % Favored : 84.10 % Rotamer: Outliers : 2.31 % Allowed : 27.22 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % 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: -3.91 (0.19), residues: 1560 helix: -0.51 (0.31), residues: 290 sheet: -2.54 (0.25), residues: 386 loop : -3.50 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 93 HIS 0.003 0.001 HIS A 280 PHE 0.020 0.001 PHE A 197 TYR 0.018 0.001 TYR A 522 ARG 0.007 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.461 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 186 average time/residue: 0.2494 time to fit residues: 68.6318 Evaluate side-chains 169 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1119 time to fit residues: 5.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.2980 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN E 52 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12509 Z= 0.168 Angle : 0.649 11.050 17003 Z= 0.335 Chirality : 0.044 0.168 1862 Planarity : 0.005 0.093 2242 Dihedral : 5.497 39.231 1725 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.45 % Favored : 84.42 % Rotamer: Outliers : 2.47 % Allowed : 27.91 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % 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: -3.67 (0.20), residues: 1560 helix: -0.28 (0.31), residues: 290 sheet: -2.43 (0.26), residues: 379 loop : -3.33 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 93 HIS 0.002 0.001 HIS A 280 PHE 0.015 0.001 PHE A 804 TYR 0.010 0.001 TYR D 36 ARG 0.006 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.538 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 185 average time/residue: 0.2231 time to fit residues: 61.7101 Evaluate side-chains 167 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1217 time to fit residues: 5.4986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 0.0060 chunk 91 optimal weight: 0.0010 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN E 36 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12509 Z= 0.158 Angle : 0.640 10.526 17003 Z= 0.331 Chirality : 0.043 0.281 1862 Planarity : 0.004 0.089 2242 Dihedral : 5.353 38.780 1725 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.38 % Favored : 84.55 % Rotamer: Outliers : 1.93 % Allowed : 28.68 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % 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: -3.48 (0.20), residues: 1560 helix: -0.12 (0.32), residues: 290 sheet: -2.21 (0.27), residues: 368 loop : -3.26 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 93 HIS 0.002 0.000 HIS B 64 PHE 0.016 0.001 PHE A 804 TYR 0.036 0.001 TYR D 107 ARG 0.007 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.473 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 184 average time/residue: 0.2202 time to fit residues: 61.0230 Evaluate side-chains 158 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.431 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1162 time to fit residues: 4.2480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 52 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12509 Z= 0.204 Angle : 0.664 11.936 17003 Z= 0.345 Chirality : 0.044 0.257 1862 Planarity : 0.005 0.086 2242 Dihedral : 5.530 39.469 1725 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.77 % Favored : 84.17 % Rotamer: Outliers : 2.00 % Allowed : 29.38 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 1.56 % Twisted General : 0.07 % 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: -3.45 (0.20), residues: 1560 helix: 0.06 (0.32), residues: 287 sheet: -2.29 (0.25), residues: 403 loop : -3.26 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.003 0.001 HIS C 51 PHE 0.018 0.001 PHE A 804 TYR 0.016 0.001 TYR A 548 ARG 0.007 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.421 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 173 average time/residue: 0.2390 time to fit residues: 62.5020 Evaluate side-chains 168 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1125 time to fit residues: 5.4040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12509 Z= 0.195 Angle : 0.665 11.195 17003 Z= 0.346 Chirality : 0.044 0.225 1862 Planarity : 0.005 0.083 2242 Dihedral : 5.549 39.487 1725 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.77 % Favored : 84.17 % Rotamer: Outliers : 1.00 % Allowed : 29.99 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 1.56 % Twisted General : 0.07 % 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: -3.37 (0.20), residues: 1560 helix: 0.09 (0.32), residues: 288 sheet: -2.16 (0.26), residues: 406 loop : -3.24 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 745 HIS 0.003 0.001 HIS A 280 PHE 0.019 0.001 PHE A 804 TYR 0.014 0.001 TYR A 548 ARG 0.007 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.418 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 169 average time/residue: 0.2513 time to fit residues: 62.5701 Evaluate side-chains 165 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1145 time to fit residues: 4.1870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 155 optimal weight: 0.3980 chunk 143 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12509 Z= 0.186 Angle : 0.672 13.259 17003 Z= 0.348 Chirality : 0.044 0.218 1862 Planarity : 0.005 0.079 2242 Dihedral : 5.540 39.337 1725 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.90 % Favored : 84.04 % Rotamer: Outliers : 0.46 % Allowed : 30.45 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 1.56 % Twisted General : 0.07 % 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: -3.33 (0.20), residues: 1560 helix: 0.03 (0.32), residues: 294 sheet: -2.12 (0.26), residues: 407 loop : -3.20 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 93 HIS 0.003 0.001 HIS C 51 PHE 0.018 0.001 PHE A 804 TYR 0.012 0.001 TYR A 548 ARG 0.007 0.000 ARG D 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 162 average time/residue: 0.2358 time to fit residues: 56.8166 Evaluate side-chains 158 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1213 time to fit residues: 2.9073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN B 144 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093749 restraints weight = 20996.597| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.06 r_work: 0.3114 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12509 Z= 0.281 Angle : 0.723 13.173 17003 Z= 0.378 Chirality : 0.046 0.224 1862 Planarity : 0.005 0.074 2242 Dihedral : 5.924 41.142 1725 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 17.18 % Favored : 82.76 % Rotamer: Outliers : 0.77 % Allowed : 30.45 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.07 % Twisted Proline : 1.56 % Twisted General : 0.13 % 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: -3.46 (0.20), residues: 1560 helix: -0.06 (0.31), residues: 299 sheet: -2.23 (0.26), residues: 405 loop : -3.30 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 745 HIS 0.005 0.001 HIS A 280 PHE 0.051 0.002 PHE A 804 TYR 0.030 0.002 TYR D 107 ARG 0.007 0.001 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.24 seconds wall clock time: 49 minutes 45.81 seconds (2985.81 seconds total)