Starting phenix.real_space_refine on Sat Dec 9 16:07:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/12_2023/7lhg_23339.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/12_2023/7lhg_23339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/12_2023/7lhg_23339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/12_2023/7lhg_23339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/12_2023/7lhg_23339.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/12_2023/7lhg_23339.pdb" } resolution = 3.8 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= 0.001 sd= 0.004 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 32 5.16 5 C 7299 2.51 5 N 2024 2.21 5 O 2237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C ASP 149": "OD1" <-> "OD2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 502": "OD1" <-> "OD2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 652": "NH1" <-> "NH2" Residue "C ARG 674": "NH1" <-> "NH2" Residue "C TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 688": "NH1" <-> "NH2" Residue "C ARG 697": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "C PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 12": "OD1" <-> "OD2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G ASP 133": "OD1" <-> "OD2" Residue "G ASP 163": "OD1" <-> "OD2" Residue "G TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 282": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11592 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 6217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6217 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 773} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1702 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain: "K" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1177 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 146} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2496 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 299} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 6.35, per 1000 atoms: 0.55 Number of scatterers: 11592 At special positions: 0 Unit cell: (99.813, 96.726, 171.843, 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 32 16.00 O 2237 8.00 N 2024 7.00 C 7299 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 28 sheets defined 4.2% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.587A pdb=" N VAL C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.658A pdb=" N LEU C 126 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 4.111A pdb=" N TYR C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.632A pdb=" N ASP D 130 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 158 Processing helix chain 'G' and resid 194 through 200 Processing helix chain 'G' and resid 232 through 237 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.730A pdb=" N TYR C 32 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 50 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL C 53 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN C 68 " --> pdb=" O VAL C 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.609A pdb=" N ASP C 35 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE C 119 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 37 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 116 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 111 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG C 118 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 107 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 467 through 469 removed outlier: 6.727A pdb=" N THR C 494 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 473 " --> pdb=" O TYR C 490 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR C 471 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 472 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 439 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 474 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 410 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 398 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 393 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 343 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR C 338 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP C 239 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 231 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 241 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 229 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 217 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE C 211 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N ASN C 230 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 14.993A pdb=" N SER C 209 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 192 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 205 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP C 186 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 211 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG C 184 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 213 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG C 182 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 153 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 151 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 634 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 641 through 643 removed outlier: 3.604A pdb=" N THR C 634 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 579 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 594 through 595 Processing sheet with id=AA6, first strand: chain 'C' and resid 594 through 595 removed outlier: 3.665A pdb=" N SER C 588 " --> pdb=" O TYR C 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 563 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 529 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 491 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 494 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 265 through 266 removed outlier: 4.040A pdb=" N GLY C 266 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 293 " --> pdb=" O GLY C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 4.190A pdb=" N SER C 277 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP C 307 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 306 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 322 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 308 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 320 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 318 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 677 through 680 removed outlier: 3.710A pdb=" N GLY C 719 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 721 " --> pdb=" O LEU C 654 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.542A pdb=" N ASN C 689 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C 711 " --> pdb=" O ASN C 689 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'C' and resid 730 through 732 Processing sheet with id=AB4, first strand: chain 'C' and resid 756 through 758 removed outlier: 3.642A pdb=" N GLY C 758 " --> pdb=" O VAL C 749 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 779 " --> pdb=" O GLN C 786 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN C 786 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP C 781 " --> pdb=" O LYS C 784 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.568A pdb=" N SER D 3 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 8 through 12 removed outlier: 6.542A pdb=" N ALA D 9 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ARG D 116 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE D 11 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.624A pdb=" N GLN D 57 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 32 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR D 109 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU D 92 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 107 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 102 " --> pdb=" O ALA K 169 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA K 171 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN D 104 " --> pdb=" O ALA K 171 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE K 173 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA D 106 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU K 175 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN D 108 " --> pdb=" O LEU K 175 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR K 177 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS D 110 " --> pdb=" O TYR K 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR K 176 " --> pdb=" O THR K 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 50 through 52 removed outlier: 4.076A pdb=" N ILE D 51 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 177 through 181 removed outlier: 3.699A pdb=" N SER D 177 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 133 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 171 through 172 removed outlier: 3.850A pdb=" N VAL D 171 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 153 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR D 152 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 194 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER D 192 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 66 through 70 removed outlier: 3.772A pdb=" N GLU K 66 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA K 148 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AC4, first strand: chain 'G' and resid 57 through 61 removed outlier: 6.914A pdb=" N PHE G 26 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 180 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 81 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS G 182 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU G 79 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 184 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 77 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG G 78 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP G 128 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS G 126 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA G 82 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY G 124 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL G 84 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU G 122 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE G 120 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 57 through 61 removed outlier: 6.914A pdb=" N PHE G 26 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 180 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 81 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS G 182 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU G 79 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 184 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 77 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 33 through 40 removed outlier: 3.578A pdb=" N TYR G 35 " --> pdb=" O LEU G 208 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 210 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS G 212 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN G 39 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE G 211 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.600A pdb=" N GLU G 101 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AC9, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AD1, first strand: chain 'G' and resid 256 through 261 removed outlier: 3.523A pdb=" N ARG G 256 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR G 330 " --> pdb=" O LEU G 260 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 915 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: 4.54 Time building geometry restraints manager: 4.43 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: 3737 1.34 - 1.46: 2826 1.46 - 1.58: 5240 1.58 - 1.70: 2 1.70 - 1.83: 52 Bond restraints: 11857 Sorted by residual: bond pdb=" C THR D 71 " pdb=" N THR D 72 " ideal model delta sigma weight residual 1.327 1.480 -0.153 1.71e-02 3.42e+03 8.01e+01 bond pdb=" C LYS D 77 " pdb=" N LEU D 78 " ideal model delta sigma weight residual 1.328 1.398 -0.070 1.14e-02 7.69e+03 3.80e+01 bond pdb=" CA LEU C 86 " pdb=" CB LEU C 86 " ideal model delta sigma weight residual 1.527 1.599 -0.072 1.75e-02 3.27e+03 1.70e+01 bond pdb=" C VAL C 288 " pdb=" N PRO C 289 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.25e-02 6.40e+03 1.18e+01 bond pdb=" CA CYS K 75 " pdb=" C CYS K 75 " ideal model delta sigma weight residual 1.522 1.565 -0.042 1.37e-02 5.33e+03 9.62e+00 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 97.09 - 107.15: 566 107.15 - 117.21: 7834 117.21 - 127.28: 7537 127.28 - 137.34: 168 137.34 - 147.40: 2 Bond angle restraints: 16107 Sorted by residual: angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 111.62 100.76 10.86 7.90e-01 1.60e+00 1.89e+02 angle pdb=" C THR D 71 " pdb=" N THR D 72 " pdb=" CA THR D 72 " ideal model delta sigma weight residual 123.15 147.40 -24.25 2.23e+00 2.01e-01 1.18e+02 angle pdb=" C TYR K 58 " pdb=" N PRO K 59 " pdb=" CA PRO K 59 " ideal model delta sigma weight residual 120.38 131.09 -10.71 1.03e+00 9.43e-01 1.08e+02 angle pdb=" N ASN C 368 " pdb=" CA ASN C 368 " pdb=" C ASN C 368 " ideal model delta sigma weight residual 110.44 99.09 11.35 1.20e+00 6.94e-01 8.94e+01 angle pdb=" CA TYR C 26 " pdb=" CB TYR C 26 " pdb=" CG TYR C 26 " ideal model delta sigma weight residual 113.90 130.59 -16.69 1.80e+00 3.09e-01 8.60e+01 ... (remaining 16102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 6140 17.08 - 34.16: 681 34.16 - 51.24: 145 51.24 - 68.32: 28 68.32 - 85.40: 14 Dihedral angle restraints: 7008 sinusoidal: 2749 harmonic: 4259 Sorted by residual: dihedral pdb=" C ASP C 481 " pdb=" N ASP C 481 " pdb=" CA ASP C 481 " pdb=" CB ASP C 481 " ideal model delta harmonic sigma weight residual -122.60 -133.64 11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" N ASP C 481 " pdb=" C ASP C 481 " pdb=" CA ASP C 481 " pdb=" CB ASP C 481 " ideal model delta harmonic sigma weight residual 122.80 132.58 -9.78 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C VAL C 7 " pdb=" N VAL C 7 " pdb=" CA VAL C 7 " pdb=" CB VAL C 7 " ideal model delta harmonic sigma weight residual -122.00 -130.96 8.96 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 7005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1295 0.084 - 0.168: 362 0.168 - 0.252: 66 0.252 - 0.336: 19 0.336 - 0.419: 5 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CA CYS D 207 " pdb=" N CYS D 207 " pdb=" C CYS D 207 " pdb=" CB CYS D 207 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CB ILE D 194 " pdb=" CA ILE D 194 " pdb=" CG1 ILE D 194 " pdb=" CG2 ILE D 194 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA TRP C 92 " pdb=" N TRP C 92 " pdb=" C TRP C 92 " pdb=" CB TRP C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1744 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 72 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 73 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 73 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 73 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 327 " 0.061 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO C 328 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 328 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 328 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 698 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO C 699 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 699 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 699 " -0.045 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3558 2.84 - 3.35: 9196 3.35 - 3.87: 19317 3.87 - 4.38: 19881 4.38 - 4.90: 35363 Nonbonded interactions: 87315 Sorted by model distance: nonbonded pdb=" O ASN G 196 " pdb=" OG1 THR G 200 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR C 72 " pdb=" OD1 ASP C 74 " model vdw 2.334 2.440 nonbonded pdb=" OG SER C 612 " pdb=" OG SER C 628 " model vdw 2.340 2.440 nonbonded pdb=" OG SER D 159 " pdb=" OE1 GLN D 162 " model vdw 2.345 2.440 nonbonded pdb=" O VAL C 1 " pdb=" OG SER C 22 " model vdw 2.353 2.440 ... (remaining 87310 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.250 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.740 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 0.153 11857 Z= 0.507 Angle : 1.665 24.249 16107 Z= 1.009 Chirality : 0.084 0.419 1747 Planarity : 0.009 0.104 2112 Dihedral : 14.921 85.404 4308 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Cbeta Deviations : 0.07 % 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: -4.42 (0.17), residues: 1482 helix: -4.64 (0.30), residues: 52 sheet: -2.41 (0.20), residues: 530 loop : -3.30 (0.15), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 781 HIS 0.026 0.004 HIS K 36 PHE 0.045 0.004 PHE G 209 TYR 0.038 0.004 TYR K 58 ARG 0.027 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2867 time to fit residues: 101.3578 Evaluate side-chains 160 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN K 43 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 11857 Z= 0.340 Angle : 0.775 10.040 16107 Z= 0.409 Chirality : 0.048 0.206 1747 Planarity : 0.006 0.100 2112 Dihedral : 5.135 54.792 1650 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.94 % Allowed : 19.55 % Favored : 76.51 % 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: -3.68 (0.19), residues: 1482 helix: -3.29 (0.58), residues: 36 sheet: -2.15 (0.20), residues: 601 loop : -2.67 (0.18), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 92 HIS 0.011 0.002 HIS G 239 PHE 0.026 0.002 PHE G 209 TYR 0.022 0.002 TYR C 471 ARG 0.009 0.001 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 160 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 26 residues processed: 197 average time/residue: 0.2509 time to fit residues: 70.4136 Evaluate side-chains 161 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1088 time to fit residues: 6.9742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 232 ASN C 560 ASN C 799 GLN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 11857 Z= 0.305 Angle : 0.751 14.057 16107 Z= 0.381 Chirality : 0.047 0.186 1747 Planarity : 0.005 0.085 2112 Dihedral : 5.036 43.113 1650 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.86 % Allowed : 23.01 % Favored : 73.13 % 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: -3.38 (0.20), residues: 1482 helix: -2.74 (0.71), residues: 39 sheet: -2.06 (0.20), residues: 609 loop : -2.38 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 133 HIS 0.021 0.003 HIS G 279 PHE 0.017 0.002 PHE G 86 TYR 0.027 0.002 TYR C 720 ARG 0.008 0.001 ARG K 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 186 average time/residue: 0.2353 time to fit residues: 64.9292 Evaluate side-chains 151 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1482 time to fit residues: 7.8485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.187 11857 Z= 0.491 Angle : 0.865 10.702 16107 Z= 0.449 Chirality : 0.051 0.215 1747 Planarity : 0.007 0.120 2112 Dihedral : 5.871 30.804 1650 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.51 % Allowed : 25.66 % Favored : 69.83 % 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: -3.43 (0.20), residues: 1482 helix: -2.81 (0.64), residues: 39 sheet: -2.18 (0.19), residues: 603 loop : -2.33 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 133 HIS 0.011 0.003 HIS G 182 PHE 0.028 0.003 PHE G 209 TYR 0.041 0.003 TYR C 720 ARG 0.014 0.001 ARG C 721 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 131 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 28 residues processed: 178 average time/residue: 0.2196 time to fit residues: 58.2021 Evaluate side-chains 139 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1129 time to fit residues: 7.6708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 69.725 > 50: distance: 61 - 63: 28.593 distance: 63 - 64: 11.460 distance: 64 - 65: 42.011 distance: 65 - 66: 9.042 distance: 65 - 74: 40.367 distance: 70 - 71: 49.319 distance: 71 - 72: 32.026 distance: 71 - 73: 39.824 distance: 74 - 75: 23.239 distance: 75 - 78: 65.198 distance: 76 - 77: 55.398 distance: 76 - 80: 56.879 distance: 78 - 79: 40.107 distance: 80 - 81: 38.595 distance: 80 - 86: 44.000 distance: 81 - 82: 5.659 distance: 81 - 84: 40.347 distance: 82 - 83: 38.759 distance: 82 - 87: 5.539 distance: 84 - 85: 56.976 distance: 85 - 86: 43.056 distance: 87 - 88: 40.608 distance: 88 - 91: 22.678 distance: 89 - 90: 4.607 distance: 89 - 94: 20.396 distance: 91 - 92: 38.355 distance: 91 - 93: 40.916 distance: 94 - 95: 21.580 distance: 95 - 96: 31.675 distance: 95 - 98: 33.164 distance: 96 - 97: 40.995 distance: 96 - 103: 40.111 distance: 98 - 99: 60.218 distance: 99 - 100: 46.822 distance: 100 - 101: 51.109 distance: 100 - 102: 42.812 distance: 103 - 104: 21.092 distance: 104 - 105: 17.604 distance: 104 - 107: 17.813 distance: 105 - 106: 40.921 distance: 107 - 108: 33.946 distance: 109 - 183: 38.102 distance: 110 - 111: 24.126 distance: 110 - 113: 39.883 distance: 111 - 112: 29.070 distance: 111 - 120: 27.382 distance: 112 - 180: 35.804 distance: 113 - 114: 39.145 distance: 114 - 115: 23.175 distance: 115 - 117: 27.282 distance: 117 - 119: 30.389 distance: 118 - 119: 42.802 distance: 120 - 121: 56.834 distance: 122 - 123: 5.092 distance: 122 - 127: 38.633 distance: 124 - 125: 40.361 distance: 124 - 126: 56.305 distance: 127 - 128: 41.018 distance: 127 - 171: 37.344 distance: 128 - 129: 40.077 distance: 128 - 131: 39.917 distance: 129 - 130: 13.168 distance: 130 - 168: 31.660 distance: 131 - 132: 51.442 distance: 132 - 134: 17.449 distance: 135 - 136: 40.212 distance: 136 - 137: 7.939 distance: 136 - 139: 24.574 distance: 137 - 146: 29.741 distance: 139 - 140: 17.710 distance: 143 - 144: 19.211 distance: 143 - 145: 40.162