Starting phenix.real_space_refine on Wed Feb 14 09:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/02_2024/7zde_14643_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/02_2024/7zde_14643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/02_2024/7zde_14643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/02_2024/7zde_14643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/02_2024/7zde_14643_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/02_2024/7zde_14643_neut_updated.pdb" } resolution = 3.17 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 5771 2.51 5 N 1586 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 2": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C ASP 391": "OD1" <-> "OD2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ASP 492": "OD1" <-> "OD2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C ARG 565": "NH1" <-> "NH2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ASP 346": "OD1" <-> "OD2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D GLU 511": "OE1" <-> "OE2" Residue "D ASP 517": "OD1" <-> "OD2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D ASP 546": "OD1" <-> "OD2" Residue "D ARG 566": "NH1" <-> "NH2" Residue "D TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 584": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9014 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 4418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4418 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4596 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'peptide': 587, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 559, None: 2} Not linked: pdbres="ILE D 588 " pdbres=" MG D 601 " Not linked: pdbres=" MG D 601 " pdbres="ANP D 602 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.38, per 1000 atoms: 0.60 Number of scatterers: 9014 At special positions: 0 Unit cell: (125.55, 75.33, 112.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 3 15.00 Mg 1 11.99 O 1625 8.00 N 1586 7.00 C 5771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 5 sheets defined 59.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'C' and resid 2 through 49 removed outlier: 3.591A pdb=" N LEU C 5 " --> pdb=" O ARG C 2 " (cutoff:3.500A) Proline residue: C 6 - end of helix removed outlier: 3.858A pdb=" N ALA C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 12 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 15 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TRP C 16 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET C 17 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 18 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 19 " --> pdb=" O TRP C 16 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 20 " --> pdb=" O MET C 17 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 21 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 24 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR C 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 30 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 32 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY C 34 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR C 37 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 38 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 39 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY C 40 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 43 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 46 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 47 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.528A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 135 removed outlier: 4.024A pdb=" N HIS C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 157 removed outlier: 3.619A pdb=" N VAL C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 187 through 215 removed outlier: 3.823A pdb=" N GLY C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU C 212 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 268 removed outlier: 3.907A pdb=" N THR C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.756A pdb=" N PHE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 302 removed outlier: 4.431A pdb=" N THR C 298 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY C 299 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 302 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 318 Processing helix chain 'C' and resid 382 through 385 No H-bonds generated for 'chain 'C' and resid 382 through 385' Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 409 through 415 removed outlier: 4.062A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 443 through 452 Processing helix chain 'C' and resid 456 through 459 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 507 through 520 removed outlier: 3.710A pdb=" N SER C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 519 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 556 through 561 Processing helix chain 'C' and resid 565 through 570 Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.684A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.539A pdb=" N ARG D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 63 through 108 removed outlier: 3.602A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 removed outlier: 3.601A pdb=" N GLN D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.509A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 removed outlier: 3.633A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASP D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 159 removed outlier: 3.919A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 163 through 184 removed outlier: 3.516A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 225 through 273 removed outlier: 3.531A pdb=" N PHE D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 310 removed outlier: 3.631A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.947A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.555A pdb=" N GLY D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 328 removed outlier: 3.673A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 397 removed outlier: 3.691A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 421 No H-bonds generated for 'chain 'D' and resid 418 through 421' Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 452 through 461 Processing helix chain 'D' and resid 488 through 499 removed outlier: 3.697A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 531 removed outlier: 3.528A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 571 Processing helix chain 'D' and resid 576 through 586 Processing sheet with id= A, first strand: chain 'C' and resid 339 through 342 Processing sheet with id= B, first strand: chain 'C' and resid 369 through 372 Processing sheet with id= C, first strand: chain 'D' and resid 370 through 372 Processing sheet with id= D, first strand: chain 'D' and resid 379 through 381 removed outlier: 6.157A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 426 " --> pdb=" O LEU D 506 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 555 through 557 removed outlier: 6.727A pdb=" N GLN D 557 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1212 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: 2.52 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2973 1.34 - 1.45: 1172 1.45 - 1.57: 4986 1.57 - 1.69: 6 1.69 - 1.80: 54 Bond restraints: 9191 Sorted by residual: bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.625 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.594 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N SER C 476 " pdb=" CA SER C 476 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.25e-02 6.40e+03 7.64e+00 bond pdb=" O5' ANP D 602 " pdb=" PA ANP D 602 " ideal model delta sigma weight residual 1.655 1.600 0.055 2.00e-02 2.50e+03 7.53e+00 bond pdb=" N ARG C 374 " pdb=" CA ARG C 374 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.26e+00 ... (remaining 9186 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.81: 188 105.81 - 112.88: 5011 112.88 - 119.95: 3200 119.95 - 127.02: 3973 127.02 - 134.09: 120 Bond angle restraints: 12492 Sorted by residual: angle pdb=" N GLU C 479 " pdb=" CA GLU C 479 " pdb=" C GLU C 479 " ideal model delta sigma weight residual 112.68 104.06 8.62 1.33e+00 5.65e-01 4.20e+01 angle pdb=" N PRO D 448 " pdb=" CA PRO D 448 " pdb=" CB PRO D 448 " ideal model delta sigma weight residual 103.33 109.86 -6.53 1.10e+00 8.26e-01 3.52e+01 angle pdb=" C ASN C 400 " pdb=" N ASP C 401 " pdb=" CA ASP C 401 " ideal model delta sigma weight residual 121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01 angle pdb=" N ARG D 192 " pdb=" CA ARG D 192 " pdb=" C ARG D 192 " ideal model delta sigma weight residual 112.93 108.18 4.75 1.33e+00 5.65e-01 1.28e+01 angle pdb=" CA LYS C 379 " pdb=" C LYS C 379 " pdb=" O LYS C 379 " ideal model delta sigma weight residual 121.84 117.93 3.91 1.16e+00 7.43e-01 1.13e+01 ... (remaining 12487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.63: 5034 19.63 - 39.26: 394 39.26 - 58.90: 43 58.90 - 78.53: 15 78.53 - 98.16: 12 Dihedral angle restraints: 5498 sinusoidal: 2174 harmonic: 3324 Sorted by residual: dihedral pdb=" CA ARG D 422 " pdb=" C ARG D 422 " pdb=" N LYS D 423 " pdb=" CA LYS D 423 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" O2' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 47.90 -50.26 98.16 1 3.00e+01 1.11e-03 1.22e+01 dihedral pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 164.59 70.84 93.75 1 3.00e+01 1.11e-03 1.14e+01 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1332 0.077 - 0.155: 111 0.155 - 0.232: 10 0.232 - 0.309: 0 0.309 - 0.386: 1 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C3' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C4' ANP D 602 " pdb=" O3' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.74 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA PRO D 448 " pdb=" N PRO D 448 " pdb=" C PRO D 448 " pdb=" CB PRO D 448 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C4' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" C5' ANP D 602 " pdb=" O4' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.45 -2.65 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1451 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 427 " 0.018 2.00e-02 2.50e+03 2.43e-02 1.47e+01 pdb=" CG TRP D 427 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 427 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 427 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 427 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 427 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 427 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 427 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 419 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO C 420 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 178 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO C 179 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.028 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 102 2.63 - 3.20: 8338 3.20 - 3.77: 13771 3.77 - 4.33: 20070 4.33 - 4.90: 32593 Nonbonded interactions: 74874 Sorted by model distance: nonbonded pdb=" NE2 GLN D 377 " pdb=" OD2 ASP D 551 " model vdw 2.067 2.520 nonbonded pdb=" OG SER D 417 " pdb=" OG SER D 420 " model vdw 2.122 2.440 nonbonded pdb=" NE1 TRP D 463 " pdb=" OE2 GLU D 526 " model vdw 2.172 2.520 nonbonded pdb=" NE2 GLN C 345 " pdb=" O THR C 347 " model vdw 2.222 2.520 nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 2.227 2.170 ... (remaining 74869 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=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: 1.520 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: 0.000 Extract box with map and model: 5.240 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.800 Find NCS groups from input model: 0.300 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.008 0.170 9191 Z= 0.509 Angle : 0.777 9.891 12492 Z= 0.431 Chirality : 0.047 0.386 1454 Planarity : 0.004 0.056 1593 Dihedral : 14.795 98.162 3354 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.23), residues: 1153 helix: -2.34 (0.17), residues: 685 sheet: -0.75 (0.75), residues: 61 loop : -1.12 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 427 HIS 0.005 0.001 HIS C 531 PHE 0.016 0.002 PHE D 66 TYR 0.014 0.002 TYR D 88 ARG 0.008 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8396 (mptt) REVERT: C 545 MET cc_start: 0.7939 (tpt) cc_final: 0.7511 (tpt) REVERT: D 15 GLN cc_start: 0.8232 (tm-30) cc_final: 0.8021 (tp-100) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3355 time to fit residues: 50.6739 Evaluate side-chains 102 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN D 115 GLN D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9191 Z= 0.231 Angle : 0.603 10.286 12492 Z= 0.299 Chirality : 0.040 0.143 1454 Planarity : 0.005 0.053 1593 Dihedral : 6.888 55.537 1293 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.43 % Allowed : 7.30 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.24), residues: 1153 helix: -0.91 (0.19), residues: 684 sheet: -0.82 (0.71), residues: 61 loop : -0.95 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 427 HIS 0.004 0.001 HIS C 531 PHE 0.008 0.001 PHE C 285 TYR 0.019 0.001 TYR D 88 ARG 0.005 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.081 Fit side-chains REVERT: C 12 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8399 (mmtt) REVERT: C 545 MET cc_start: 0.7886 (tpt) cc_final: 0.7576 (mmm) REVERT: C 549 GLN cc_start: 0.7764 (mp-120) cc_final: 0.7412 (mp10) REVERT: D 492 GLN cc_start: 0.8374 (tp40) cc_final: 0.8026 (mm-40) outliers start: 4 outliers final: 2 residues processed: 124 average time/residue: 0.3047 time to fit residues: 48.8367 Evaluate side-chains 106 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 529 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9191 Z= 0.193 Angle : 0.537 9.782 12492 Z= 0.265 Chirality : 0.038 0.141 1454 Planarity : 0.004 0.049 1593 Dihedral : 5.248 45.135 1293 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.75 % Allowed : 9.98 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1153 helix: 0.16 (0.20), residues: 684 sheet: -1.01 (0.68), residues: 61 loop : -0.88 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 81 HIS 0.003 0.001 HIS C 531 PHE 0.008 0.001 PHE D 327 TYR 0.019 0.001 TYR D 88 ARG 0.004 0.000 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.082 Fit side-chains REVERT: C 12 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8321 (mmtt) REVERT: C 545 MET cc_start: 0.7926 (tpt) cc_final: 0.7675 (tpt) REVERT: D 84 GLU cc_start: 0.7457 (tp30) cc_final: 0.7084 (tp30) REVERT: D 195 PHE cc_start: 0.7990 (t80) cc_final: 0.7784 (t80) outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.2810 time to fit residues: 43.2423 Evaluate side-chains 107 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.0050 chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 29 optimal weight: 0.0570 chunk 92 optimal weight: 0.8980 overall best weight: 0.7916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN D 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9191 Z= 0.204 Angle : 0.527 9.442 12492 Z= 0.259 Chirality : 0.039 0.141 1454 Planarity : 0.004 0.049 1593 Dihedral : 4.751 48.173 1293 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.39 % Allowed : 11.59 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1153 helix: 0.62 (0.20), residues: 690 sheet: -0.95 (0.62), residues: 71 loop : -0.88 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.008 0.001 PHE C 285 TYR 0.019 0.001 TYR D 88 ARG 0.012 0.000 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.173 Fit side-chains REVERT: C 12 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8305 (mmtt) REVERT: C 452 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7669 (ttp80) REVERT: D 195 PHE cc_start: 0.8007 (t80) cc_final: 0.7793 (t80) REVERT: D 460 ASP cc_start: 0.7505 (m-30) cc_final: 0.7303 (m-30) outliers start: 13 outliers final: 10 residues processed: 124 average time/residue: 0.2728 time to fit residues: 45.1738 Evaluate side-chains 117 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN D 280 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9191 Z= 0.349 Angle : 0.589 9.381 12492 Z= 0.288 Chirality : 0.042 0.164 1454 Planarity : 0.004 0.050 1593 Dihedral : 4.937 52.359 1293 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.50 % Allowed : 13.30 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1153 helix: 0.45 (0.20), residues: 694 sheet: -1.15 (0.73), residues: 56 loop : -0.95 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 81 HIS 0.004 0.001 HIS C 531 PHE 0.012 0.001 PHE C 285 TYR 0.021 0.001 TYR D 88 ARG 0.005 0.000 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.064 Fit side-chains REVERT: C 12 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8324 (mmtt) REVERT: C 452 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7764 (mtp85) REVERT: C 519 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: C 520 MET cc_start: 0.8481 (mmm) cc_final: 0.8008 (mmm) REVERT: C 549 GLN cc_start: 0.7544 (mp-120) cc_final: 0.7128 (mp10) outliers start: 14 outliers final: 11 residues processed: 113 average time/residue: 0.2848 time to fit residues: 42.4137 Evaluate side-chains 112 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9191 Z= 0.176 Angle : 0.513 9.625 12492 Z= 0.251 Chirality : 0.038 0.140 1454 Planarity : 0.003 0.045 1593 Dihedral : 4.757 54.138 1293 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.61 % Allowed : 13.73 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1153 helix: 0.88 (0.21), residues: 694 sheet: -0.92 (0.61), residues: 71 loop : -0.92 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 81 HIS 0.002 0.001 HIS C 531 PHE 0.008 0.001 PHE C 291 TYR 0.019 0.001 TYR D 88 ARG 0.004 0.000 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.995 Fit side-chains REVERT: C 12 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8299 (mmtt) REVERT: C 452 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7721 (mtp85) REVERT: C 519 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7273 (pm20) REVERT: C 520 MET cc_start: 0.8362 (mmm) cc_final: 0.8025 (mmp) REVERT: C 545 MET cc_start: 0.8398 (mmm) cc_final: 0.8143 (mmm) REVERT: C 549 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: D 195 PHE cc_start: 0.8001 (t80) cc_final: 0.7798 (t80) outliers start: 15 outliers final: 9 residues processed: 121 average time/residue: 0.2731 time to fit residues: 43.4175 Evaluate side-chains 117 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9191 Z= 0.235 Angle : 0.535 9.927 12492 Z= 0.261 Chirality : 0.039 0.141 1454 Planarity : 0.004 0.049 1593 Dihedral : 4.789 55.062 1293 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.61 % Allowed : 13.95 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1153 helix: 0.89 (0.20), residues: 694 sheet: -1.64 (0.69), residues: 47 loop : -0.89 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.010 0.001 PHE C 285 TYR 0.020 0.001 TYR D 88 ARG 0.004 0.000 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.037 Fit side-chains REVERT: C 12 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8296 (mmtt) REVERT: C 452 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7719 (mtp85) REVERT: C 519 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: C 520 MET cc_start: 0.8368 (mmm) cc_final: 0.8004 (mmp) REVERT: C 549 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: D 427 TRP cc_start: 0.6450 (p-90) cc_final: 0.6182 (p-90) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 0.2949 time to fit residues: 46.9145 Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9191 Z= 0.184 Angle : 0.511 10.395 12492 Z= 0.251 Chirality : 0.038 0.154 1454 Planarity : 0.003 0.044 1593 Dihedral : 4.716 56.282 1293 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.50 % Allowed : 14.27 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1153 helix: 1.09 (0.20), residues: 694 sheet: -1.39 (0.64), residues: 57 loop : -0.84 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.003 0.001 HIS D 204 PHE 0.008 0.001 PHE D 327 TYR 0.020 0.001 TYR D 88 ARG 0.005 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.982 Fit side-chains REVERT: C 12 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8269 (mmtt) REVERT: C 452 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7704 (mtp85) REVERT: C 519 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: C 520 MET cc_start: 0.8313 (mmm) cc_final: 0.7945 (mmp) REVERT: C 549 GLN cc_start: 0.7413 (mp10) cc_final: 0.7121 (mp10) REVERT: D 195 PHE cc_start: 0.8008 (t80) cc_final: 0.7804 (t80) REVERT: D 350 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8258 (mt) REVERT: D 427 TRP cc_start: 0.6440 (p-90) cc_final: 0.6161 (p-90) outliers start: 14 outliers final: 11 residues processed: 121 average time/residue: 0.2717 time to fit residues: 43.2627 Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9191 Z= 0.291 Angle : 0.565 10.476 12492 Z= 0.275 Chirality : 0.041 0.163 1454 Planarity : 0.004 0.049 1593 Dihedral : 4.855 57.021 1293 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.61 % Allowed : 14.81 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1153 helix: 0.89 (0.20), residues: 698 sheet: -1.40 (0.69), residues: 47 loop : -0.94 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE C 285 TYR 0.020 0.001 TYR D 88 ARG 0.012 0.000 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.114 Fit side-chains REVERT: C 12 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8297 (mmtt) REVERT: C 452 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7717 (mtp85) REVERT: C 519 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: C 520 MET cc_start: 0.8351 (mmm) cc_final: 0.7945 (mmp) REVERT: C 549 GLN cc_start: 0.7580 (mp10) cc_final: 0.7178 (mp10) REVERT: D 350 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8314 (mt) REVERT: D 427 TRP cc_start: 0.6442 (p-90) cc_final: 0.6097 (p-90) outliers start: 15 outliers final: 12 residues processed: 116 average time/residue: 0.2821 time to fit residues: 42.8998 Evaluate side-chains 118 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9191 Z= 0.183 Angle : 0.526 10.597 12492 Z= 0.255 Chirality : 0.038 0.162 1454 Planarity : 0.004 0.044 1593 Dihedral : 4.757 58.706 1293 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.50 % Allowed : 15.02 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1153 helix: 1.20 (0.21), residues: 695 sheet: -1.21 (0.65), residues: 57 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.003 0.001 HIS D 204 PHE 0.009 0.001 PHE D 327 TYR 0.020 0.001 TYR D 88 ARG 0.011 0.000 ARG C 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.062 Fit side-chains REVERT: C 12 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8263 (mmtt) REVERT: C 431 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7604 (mtp-110) REVERT: C 452 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7807 (mtm180) REVERT: C 503 GLU cc_start: 0.7313 (tt0) cc_final: 0.7043 (tt0) REVERT: C 519 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: C 549 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: D 195 PHE cc_start: 0.8012 (t80) cc_final: 0.7810 (t80) REVERT: D 350 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8296 (mt) REVERT: D 378 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7457 (ptm160) outliers start: 14 outliers final: 10 residues processed: 121 average time/residue: 0.2858 time to fit residues: 45.1486 Evaluate side-chains 123 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 0.0170 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099706 restraints weight = 10328.866| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.61 r_work: 0.2876 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 9191 Z= 0.238 Angle : 0.945 59.172 12492 Z= 0.531 Chirality : 0.039 0.223 1454 Planarity : 0.004 0.044 1593 Dihedral : 4.758 58.712 1293 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.50 % Allowed : 15.02 % Favored : 83.48 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1153 helix: 1.21 (0.20), residues: 695 sheet: -1.20 (0.65), residues: 57 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.003 0.001 HIS D 204 PHE 0.008 0.001 PHE D 327 TYR 0.020 0.001 TYR D 88 ARG 0.007 0.000 ARG C 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.54 seconds wall clock time: 38 minutes 57.87 seconds (2337.87 seconds total)