Starting phenix.real_space_refine on Sun Dec 10 22:49:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/12_2023/7jr7_22443.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/12_2023/7jr7_22443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/12_2023/7jr7_22443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/12_2023/7jr7_22443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/12_2023/7jr7_22443.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/12_2023/7jr7_22443.pdb" } resolution = 3.3 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= 0.003 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 87 5.16 5 C 10115 2.51 5 N 2657 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B ASP 636": "OD1" <-> "OD2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1": "OD1" <-> "OD2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D ASP 185": "OD1" <-> "OD2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F ASP 143": "OD1" <-> "OD2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15799 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4626 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 2 Chain: "B" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4609 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 24, 'TRANS': 554} Chain breaks: 3 Chain: "C" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1638 Classifications: {'peptide': 210} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1627 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1663 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202} Time building chain proxies: 8.56, per 1000 atoms: 0.54 Number of scatterers: 15799 At special positions: 0 Unit cell: (158.82, 158.82, 130.232, 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 87 16.00 O 2940 8.00 N 2657 7.00 C 10115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 204 " distance=2.05 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.04 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: 5.87 Conformation dependent library (CDL) restraints added in 3.0 seconds 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3772 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 25 sheets defined 40.0% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 121 through 127 removed outlier: 4.604A pdb=" N GLN A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.565A pdb=" N GLN A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.623A pdb=" N GLY A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.807A pdb=" N GLN A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 331 removed outlier: 3.588A pdb=" N LYS A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.678A pdb=" N LYS A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 404 removed outlier: 5.443A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 455 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.768A pdb=" N MET A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.705A pdb=" N VAL A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 522 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 546 removed outlier: 3.515A pdb=" N VAL A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 4.014A pdb=" N MET A 555 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 566 through 581 removed outlier: 4.218A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.630A pdb=" N PHE A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 Processing helix chain 'A' and resid 619 through 628 Processing helix chain 'A' and resid 629 through 646 removed outlier: 3.573A pdb=" N ALA A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 228 removed outlier: 4.226A pdb=" N GLN B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 261 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 326 Processing helix chain 'B' and resid 331 through 353 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.583A pdb=" N PHE B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 360' Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 removed outlier: 3.514A pdb=" N LEU B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.814A pdb=" N VAL B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 488 through 499 removed outlier: 3.626A pdb=" N TYR B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 519 removed outlier: 4.048A pdb=" N ALA B 506 " --> pdb=" O PRO B 502 " (cutoff:3.500A) Proline residue: B 514 - end of helix Processing helix chain 'B' and resid 524 through 551 removed outlier: 3.586A pdb=" N PHE B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.719A pdb=" N VAL B 593 " --> pdb=" O TRP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 Processing helix chain 'B' and resid 625 through 633 Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.582A pdb=" N THR C 91 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.795A pdb=" N ALA D 84 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.520A pdb=" N ARG E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 6.660A pdb=" N GLU A 112 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.123A pdb=" N TYR A 45 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.197A pdb=" N MET A 82 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 96 removed outlier: 3.647A pdb=" N ASN B 90 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU B 52 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 92 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B 50 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 94 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU B 48 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG B 96 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 46 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 52 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER B 129 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR B 54 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 127 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.479A pdb=" N LEU B 101 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 283 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 294 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 285 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.531A pdb=" N SER C 69 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.644A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.973A pdb=" N CYS C 96 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP C 109 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG C 98 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 105 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.027A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER C 184 " --> pdb=" O PRO C 173 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER C 186 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N THR C 171 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.372A pdb=" N THR D 70 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N SER D 27 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N SER D 68 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ALA D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 11.853A pdb=" N SER D 66 " --> pdb=" O ALA D 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.682A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'D' and resid 115 through 119 removed outlier: 4.840A pdb=" N SER D 132 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU D 182 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL D 134 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA D 180 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE D 136 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER D 178 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN D 138 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET D 176 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.489A pdb=" N ILE E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 133 removed outlier: 4.346A pdb=" N GLY E 148 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR E 184 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER E 187 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER E 189 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 174 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR E 191 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E 172 " --> pdb=" O THR E 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 163 Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.417A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.928A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 114 through 118 removed outlier: 4.730A pdb=" N SER F 131 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU F 181 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL F 133 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU F 179 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE F 135 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER F 177 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN F 137 " --> pdb=" O MET F 175 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET F 175 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 153 through 154 830 hydrogen bonds defined for protein. 2271 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: 5.65 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4790 1.34 - 1.47: 4216 1.47 - 1.59: 7029 1.59 - 1.72: 0 1.72 - 1.84: 136 Bond restraints: 16171 Sorted by residual: bond pdb=" CG LEU E 37 " pdb=" CD1 LEU E 37 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.82e+00 bond pdb=" CG1 ILE B 403 " pdb=" CD1 ILE B 403 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.93e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.333 1.373 -0.039 1.44e-02 4.82e+03 7.48e+00 bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.333 1.370 -0.037 1.44e-02 4.82e+03 6.63e+00 bond pdb=" CG LEU B 486 " pdb=" CD2 LEU B 486 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.12e+00 ... (remaining 16166 not shown) Histogram of bond angle deviations from ideal: 96.85 - 105.24: 374 105.24 - 113.63: 8870 113.63 - 122.02: 9408 122.02 - 130.41: 3203 130.41 - 138.80: 104 Bond angle restraints: 21959 Sorted by residual: angle pdb=" N GLY E 104 " pdb=" CA GLY E 104 " pdb=" C GLY E 104 " ideal model delta sigma weight residual 112.34 128.50 -16.16 2.04e+00 2.40e-01 6.27e+01 angle pdb=" C ARG F 211 " pdb=" N ALA F 212 " pdb=" CA ALA F 212 " ideal model delta sigma weight residual 121.70 135.22 -13.52 1.80e+00 3.09e-01 5.64e+01 angle pdb=" C ARG C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta sigma weight residual 122.74 133.50 -10.76 1.44e+00 4.82e-01 5.58e+01 angle pdb=" C THR B 287 " pdb=" N SER B 288 " pdb=" CA SER B 288 " ideal model delta sigma weight residual 120.81 132.74 -11.93 1.63e+00 3.76e-01 5.36e+01 angle pdb=" CA CYS F 134 " pdb=" CB CYS F 134 " pdb=" SG CYS F 134 " ideal model delta sigma weight residual 114.40 129.93 -15.53 2.30e+00 1.89e-01 4.56e+01 ... (remaining 21954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9075 17.64 - 35.28: 411 35.28 - 52.92: 104 52.92 - 70.55: 28 70.55 - 88.19: 12 Dihedral angle restraints: 9630 sinusoidal: 3763 harmonic: 5867 Sorted by residual: dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 195 " pdb=" CB CYS D 195 " ideal model delta sinusoidal sigma weight residual 93.00 170.39 -77.39 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS F 134 " pdb=" SG CYS F 134 " pdb=" SG CYS F 194 " pdb=" CB CYS F 194 " ideal model delta sinusoidal sigma weight residual 93.00 159.01 -66.01 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" C ILE B 459 " pdb=" N ILE B 459 " pdb=" CA ILE B 459 " pdb=" CB ILE B 459 " ideal model delta harmonic sigma weight residual -122.00 -133.10 11.10 0 2.50e+00 1.60e-01 1.97e+01 ... (remaining 9627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2208 0.112 - 0.225: 264 0.225 - 0.337: 30 0.337 - 0.450: 0 0.450 - 0.562: 1 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CG LEU D 34 " pdb=" CB LEU D 34 " pdb=" CD1 LEU D 34 " pdb=" CD2 LEU D 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CB ILE A 81 " pdb=" CA ILE A 81 " pdb=" CG1 ILE A 81 " pdb=" CG2 ILE A 81 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE B 235 " pdb=" CA ILE B 235 " pdb=" CG1 ILE B 235 " pdb=" CG2 ILE B 235 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2500 not shown) Planarity restraints: 2763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 189 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL C 189 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL C 189 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO C 190 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 617 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C THR A 617 " -0.058 2.00e-02 2.50e+03 pdb=" O THR A 617 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 618 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 49 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C SER F 49 " 0.057 2.00e-02 2.50e+03 pdb=" O SER F 49 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA F 50 " -0.020 2.00e-02 2.50e+03 ... (remaining 2760 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3170 2.78 - 3.31: 14434 3.31 - 3.84: 26231 3.84 - 4.37: 29867 4.37 - 4.90: 53606 Nonbonded interactions: 127308 Sorted by model distance: nonbonded pdb=" OG SER D 122 " pdb=" OE1 GLU D 124 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR B 287 " pdb=" O THR B 325 " model vdw 2.258 2.440 nonbonded pdb=" NZ LYS B 605 " pdb=" O TYR B 638 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG B 164 " pdb=" OE2 GLU B 189 " model vdw 2.267 2.520 nonbonded pdb=" O GLY C 163 " pdb=" OG SER C 166 " model vdw 2.268 2.440 ... (remaining 127303 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: 2.490 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: 0.020 Extract box with map and model: 10.950 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 43.890 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.010 0.110 16171 Z= 0.635 Angle : 1.338 16.156 21959 Z= 0.748 Chirality : 0.076 0.562 2503 Planarity : 0.008 0.041 2763 Dihedral : 11.829 88.193 5831 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.56 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 4.99 % Favored : 94.44 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 11.46 % 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: 0.62 (0.18), residues: 1994 helix: 0.78 (0.18), residues: 727 sheet: 0.76 (0.23), residues: 475 loop : -0.00 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B 229 HIS 0.012 0.003 HIS E 57 PHE 0.054 0.005 PHE C 83 TYR 0.049 0.005 TYR B 472 ARG 0.013 0.002 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 327 time to evaluate : 1.636 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 336 average time/residue: 0.3362 time to fit residues: 160.7384 Evaluate side-chains 199 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 194 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1409 time to fit residues: 3.7026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 155 optimal weight: 40.0000 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN A 392 GLN A 393 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN A 578 ASN B 55 GLN B 89 GLN B 250 ASN C 78 GLN C 202 ASN D 54 ASN E 5 GLN E 43 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN F 166 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16171 Z= 0.233 Angle : 0.677 10.337 21959 Z= 0.362 Chirality : 0.045 0.225 2503 Planarity : 0.006 0.130 2763 Dihedral : 4.677 32.513 2191 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.41 % Favored : 97.44 % Rotamer: Outliers : 2.44 % Allowed : 9.13 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.06 (0.19), residues: 1994 helix: 1.49 (0.19), residues: 731 sheet: 0.88 (0.23), residues: 497 loop : -0.09 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 229 HIS 0.005 0.001 HIS A 510 PHE 0.024 0.002 PHE C 83 TYR 0.031 0.002 TYR B 472 ARG 0.014 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 1.568 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 239 average time/residue: 0.2748 time to fit residues: 99.4290 Evaluate side-chains 208 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1563 time to fit residues: 8.9669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS B 153 GLN B 299 HIS B 526 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 166 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16171 Z= 0.338 Angle : 0.677 10.242 21959 Z= 0.356 Chirality : 0.046 0.215 2503 Planarity : 0.005 0.051 2763 Dihedral : 4.749 35.228 2191 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % Rotamer: Outliers : 2.04 % Allowed : 11.51 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.83 (0.19), residues: 1994 helix: 1.31 (0.19), residues: 738 sheet: 0.86 (0.23), residues: 500 loop : -0.33 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 109 HIS 0.009 0.001 HIS B 150 PHE 0.023 0.002 PHE B 493 TYR 0.032 0.002 TYR B 472 ARG 0.005 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 1.797 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 215 average time/residue: 0.2779 time to fit residues: 90.6836 Evaluate side-chains 199 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.894 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1495 time to fit residues: 8.1479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 6.9990 chunk 136 optimal weight: 0.5980 chunk 93 optimal weight: 0.0040 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS A 531 ASN B 504 HIS B 520 ASN C 5 GLN E 57 HIS F 89 GLN F 166 GLN F 210 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16171 Z= 0.162 Angle : 0.576 8.505 21959 Z= 0.300 Chirality : 0.042 0.182 2503 Planarity : 0.004 0.043 2763 Dihedral : 4.433 35.343 2191 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 1.08 % Allowed : 12.42 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.04 (0.19), residues: 1994 helix: 1.65 (0.19), residues: 740 sheet: 0.88 (0.23), residues: 501 loop : -0.35 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 584 HIS 0.009 0.001 HIS B 438 PHE 0.020 0.001 PHE A 608 TYR 0.026 0.001 TYR E 107 ARG 0.005 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.914 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 215 average time/residue: 0.2766 time to fit residues: 90.2466 Evaluate side-chains 202 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1829 time to fit residues: 5.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16171 Z= 0.400 Angle : 0.691 9.310 21959 Z= 0.360 Chirality : 0.047 0.183 2503 Planarity : 0.005 0.061 2763 Dihedral : 4.833 33.399 2191 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 1.87 % Allowed : 13.22 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1994 helix: 1.20 (0.19), residues: 738 sheet: 0.87 (0.23), residues: 505 loop : -0.62 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 109 HIS 0.007 0.001 HIS A 510 PHE 0.028 0.003 PHE C 83 TYR 0.030 0.002 TYR B 472 ARG 0.006 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 215 average time/residue: 0.3017 time to fit residues: 98.5751 Evaluate side-chains 205 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2982 time to fit residues: 15.3193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN E 84 ASN F 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16171 Z= 0.181 Angle : 0.570 9.486 21959 Z= 0.296 Chirality : 0.042 0.182 2503 Planarity : 0.004 0.044 2763 Dihedral : 4.495 35.614 2191 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 1.13 % Allowed : 14.01 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.92 (0.19), residues: 1994 helix: 1.60 (0.19), residues: 740 sheet: 0.97 (0.23), residues: 493 loop : -0.59 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 584 HIS 0.004 0.001 HIS F 189 PHE 0.015 0.001 PHE A 608 TYR 0.020 0.001 TYR E 154 ARG 0.004 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 1.843 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 201 average time/residue: 0.3001 time to fit residues: 92.4531 Evaluate side-chains 195 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 2.176 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1988 time to fit residues: 6.3599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN F 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16171 Z= 0.246 Angle : 0.592 10.699 21959 Z= 0.307 Chirality : 0.043 0.183 2503 Planarity : 0.005 0.045 2763 Dihedral : 4.489 34.207 2191 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 0.85 % Allowed : 14.92 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.91 (0.19), residues: 1994 helix: 1.62 (0.19), residues: 741 sheet: 0.98 (0.23), residues: 495 loop : -0.65 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 160 HIS 0.005 0.001 HIS B 150 PHE 0.018 0.002 PHE A 403 TYR 0.020 0.002 TYR B 571 ARG 0.006 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.641 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 193 average time/residue: 0.2736 time to fit residues: 80.1337 Evaluate side-chains 188 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1598 time to fit residues: 5.1266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 0.0020 chunk 150 optimal weight: 8.9990 chunk 174 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN C 82 GLN F 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16171 Z= 0.158 Angle : 0.555 9.231 21959 Z= 0.287 Chirality : 0.041 0.178 2503 Planarity : 0.004 0.043 2763 Dihedral : 4.279 34.554 2191 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 0.62 % Allowed : 15.14 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 1994 helix: 1.86 (0.19), residues: 738 sheet: 1.04 (0.24), residues: 490 loop : -0.53 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 584 HIS 0.002 0.000 HIS A 510 PHE 0.015 0.001 PHE A 608 TYR 0.020 0.001 TYR B 571 ARG 0.006 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 1.726 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 193 average time/residue: 0.2951 time to fit residues: 86.6882 Evaluate side-chains 189 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1916 time to fit residues: 4.8849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.0670 chunk 167 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16171 Z= 0.215 Angle : 0.572 12.075 21959 Z= 0.294 Chirality : 0.042 0.181 2503 Planarity : 0.005 0.044 2763 Dihedral : 4.306 33.652 2191 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 0.45 % Allowed : 15.66 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.10 (0.19), residues: 1994 helix: 1.82 (0.19), residues: 740 sheet: 1.07 (0.24), residues: 486 loop : -0.56 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 160 HIS 0.004 0.001 HIS B 150 PHE 0.015 0.001 PHE A 403 TYR 0.020 0.001 TYR E 131 ARG 0.007 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 1.861 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 191 average time/residue: 0.2814 time to fit residues: 81.9295 Evaluate side-chains 188 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1467 time to fit residues: 3.7189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.8847 > 50: distance: 20 - 25: 16.840 distance: 25 - 26: 14.320 distance: 26 - 27: 12.240 distance: 26 - 29: 10.212 distance: 27 - 28: 17.750 distance: 27 - 35: 8.487 distance: 29 - 30: 11.052 distance: 30 - 31: 4.027 distance: 30 - 32: 8.571 distance: 31 - 33: 7.366 distance: 32 - 34: 3.649 distance: 33 - 34: 12.339 distance: 35 - 36: 15.871 distance: 36 - 37: 27.750 distance: 36 - 39: 39.692 distance: 37 - 38: 25.739 distance: 37 - 42: 21.924 distance: 39 - 40: 14.831 distance: 39 - 41: 33.176 distance: 42 - 43: 22.256 distance: 43 - 44: 12.391 distance: 43 - 46: 10.169 distance: 44 - 45: 12.909 distance: 44 - 53: 16.223 distance: 46 - 47: 19.594 distance: 47 - 48: 10.315 distance: 47 - 49: 29.624 distance: 48 - 50: 13.864 distance: 49 - 51: 6.986 distance: 50 - 52: 32.218 distance: 51 - 52: 22.477 distance: 53 - 54: 14.160 distance: 53 - 59: 21.356 distance: 54 - 55: 11.156 distance: 54 - 57: 23.206 distance: 55 - 56: 22.092 distance: 55 - 60: 10.166 distance: 57 - 58: 31.629 distance: 58 - 59: 11.910 distance: 60 - 61: 9.132 distance: 61 - 62: 32.200 distance: 61 - 64: 13.914 distance: 62 - 63: 18.583 distance: 62 - 65: 20.413 distance: 65 - 66: 15.663 distance: 65 - 124: 9.237 distance: 66 - 67: 17.462 distance: 66 - 69: 19.535 distance: 67 - 68: 32.929 distance: 67 - 72: 7.531 distance: 68 - 121: 19.963 distance: 69 - 70: 20.702 distance: 69 - 71: 36.408 distance: 72 - 73: 9.089 distance: 73 - 74: 10.723 distance: 73 - 76: 14.757 distance: 74 - 75: 17.376 distance: 74 - 80: 11.025 distance: 76 - 77: 18.562 distance: 77 - 78: 11.364 distance: 77 - 79: 16.033 distance: 80 - 81: 11.319 distance: 80 - 106: 5.952 distance: 81 - 82: 12.865 distance: 82 - 83: 13.879 distance: 82 - 89: 10.755 distance: 83 - 103: 26.551 distance: 84 - 85: 19.863 distance: 85 - 86: 6.393 distance: 86 - 87: 8.845 distance: 86 - 88: 11.233 distance: 89 - 90: 5.777 distance: 90 - 91: 29.054 distance: 90 - 93: 10.782 distance: 91 - 92: 12.850 distance: 91 - 95: 13.816 distance: 93 - 94: 18.385 distance: 95 - 96: 27.120 distance: 96 - 97: 34.100 distance: 97 - 98: 7.795 distance: 97 - 103: 31.322 distance: 99 - 100: 32.601 distance: 100 - 101: 22.949 distance: 100 - 102: 24.024