Starting phenix.real_space_refine (version: dev) on Sun May 15 04:50:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/05_2022/7pme_13530_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/05_2022/7pme_13530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/05_2022/7pme_13530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/05_2022/7pme_13530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/05_2022/7pme_13530_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/05_2022/7pme_13530_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 35": "OD1" <-> "OD2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 511": "OE1" <-> "OE2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 674": "OD1" <-> "OD2" Residue "D PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ASP 723": "OD1" <-> "OD2" Residue "D ARG 724": "NH1" <-> "NH2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 789": "NH1" <-> "NH2" Residue "D ARG 792": "NH1" <-> "NH2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 154": "OD1" <-> "OD2" Residue "G GLU 195": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 23370 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 1, 'DTH_chir_02_both': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 1, 'DTH_chir_02_both': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 1, 'DTH_chir_02_both': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.94, per 1000 atoms: 0.55 Number of scatterers: 23370 At special positions: 0 Unit cell: (169.4, 209, 182.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 12 15.00 Mg 7 11.99 O 4389 8.00 N 3963 7.00 C 14851 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: 9.31 Conformation dependent library (CDL) restraints added in 3.6 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 5464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 30 sheets defined 48.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.542A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 270 removed outlier: 5.022A pdb=" N ALA A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 4.122A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.618A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 301 through 314 removed outlier: 3.887A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.676A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.767A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.591A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.635A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 714 removed outlier: 5.877A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.857A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 753 through 791 removed outlier: 4.763A pdb=" N ALA A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.266A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.378A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.610A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.743A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 253 through 261 Proline residue: C 258 - end of helix removed outlier: 4.724A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.729A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.674A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.107A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.769A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.637A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 139 through 152 removed outlier: 3.555A pdb=" N GLU D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 184 Processing helix chain 'D' and resid 192 through 207 removed outlier: 3.624A pdb=" N ASN D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 246 through 249 Processing helix chain 'D' and resid 260 through 270 removed outlier: 5.012A pdb=" N ALA D 270 " --> pdb=" O CYS D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 removed outlier: 4.065A pdb=" N THR D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.667A pdb=" N GLN D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLY D 291 " --> pdb=" O TYR D 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 286 through 291' Processing helix chain 'D' and resid 301 through 314 removed outlier: 3.887A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 337 removed outlier: 3.646A pdb=" N ASN D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 368 through 374 Processing helix chain 'D' and resid 393 through 423 Processing helix chain 'D' and resid 449 through 479 Processing helix chain 'D' and resid 484 through 486 No H-bonds generated for 'chain 'D' and resid 484 through 486' Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.754A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 531 Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.580A pdb=" N LEU D 580 " --> pdb=" O GLN D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 636 through 652 Processing helix chain 'D' and resid 675 through 684 removed outlier: 3.655A pdb=" N GLN D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 695 Processing helix chain 'D' and resid 704 through 714 removed outlier: 5.984A pdb=" N VAL D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 735 removed outlier: 3.789A pdb=" N GLU D 733 " --> pdb=" O LYS D 729 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 734 " --> pdb=" O ASN D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 741 No H-bonds generated for 'chain 'D' and resid 739 through 741' Processing helix chain 'D' and resid 753 through 791 removed outlier: 4.735A pdb=" N ALA D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 29 through 38 removed outlier: 4.155A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 78 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 87 through 96 removed outlier: 4.366A pdb=" N PHE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.647A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 184 through 196 removed outlier: 3.703A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 253 through 261 Proline residue: F 258 - end of helix removed outlier: 4.757A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 274 through 284 removed outlier: 3.684A pdb=" N LYS F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.122A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 removed outlier: 3.770A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.612A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.599A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 184 through 196 removed outlier: 3.697A pdb=" N LYS G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 253 through 261 Proline residue: G 258 - end of helix removed outlier: 4.720A pdb=" N LEU G 261 " --> pdb=" O CYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 274 through 284 removed outlier: 3.712A pdb=" N LYS G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 294 removed outlier: 4.644A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 305 Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.085A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY G 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA G 347 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 3.787A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 373 removed outlier: 3.589A pdb=" N LYS G 373 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 16 Processing sheet with id= B, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= C, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.791A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= E, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= F, first strand: chain 'A' and resid 700 through 703 Processing sheet with id= G, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.240A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= I, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= J, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.764A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.728A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= N, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.096A pdb=" N ALA D 11 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 37 through 41 Processing sheet with id= P, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.901A pdb=" N GLY D 163 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 377 through 382 Processing sheet with id= R, first strand: chain 'D' and resid 547 through 551 Processing sheet with id= S, first strand: chain 'D' and resid 700 through 703 Processing sheet with id= T, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.235A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 26 through 28 Processing sheet with id= V, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.803A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS F 18 " --> pdb=" O ASP F 11 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= X, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.745A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Z, first strand: chain 'G' and resid 8 through 11 removed outlier: 3.600A pdb=" N LYS G 18 " --> pdb=" O ASP G 11 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 35 through 38 Processing sheet with id= AB, first strand: chain 'G' and resid 103 through 107 Processing sheet with id= AC, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.774A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 971 hydrogen bonds defined for protein. 2703 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: 8.18 Time building geometry restraints manager: 10.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3908 1.32 - 1.44: 6297 1.44 - 1.57: 13398 1.57 - 1.69: 20 1.69 - 1.81: 243 Bond restraints: 23866 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" O3A ANP D1901 " pdb=" PB ANP D1901 " ideal model delta sigma weight residual 1.700 1.561 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 23861 not shown) Histogram of bond angle deviations from ideal: 98.63 - 106.23: 694 106.23 - 113.82: 13305 113.82 - 121.42: 12883 121.42 - 129.01: 5229 129.01 - 136.61: 154 Bond angle restraints: 32265 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 108.12 18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" PB ANP D1901 " pdb=" N3B ANP D1901 " pdb=" PG ANP D1901 " ideal model delta sigma weight residual 126.95 108.67 18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta sigma weight residual 121.70 111.27 10.43 1.80e+00 3.09e-01 3.36e+01 angle pdb=" C HYP I 6 " pdb=" N ALA I 7 " pdb=" CA ALA I 7 " ideal model delta sigma weight residual 121.70 111.63 10.07 1.80e+00 3.09e-01 3.13e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 112.16 9.54 1.80e+00 3.09e-01 2.81e+01 ... (remaining 32260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.36: 13756 25.36 - 50.73: 451 50.73 - 76.09: 87 76.09 - 101.46: 37 101.46 - 126.82: 9 Dihedral angle restraints: 14340 sinusoidal: 5861 harmonic: 8479 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.18 126.82 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.24 126.76 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.27 126.74 1 2.00e+01 2.50e-03 3.84e+01 ... (remaining 14337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2816 0.056 - 0.112: 600 0.112 - 0.168: 105 0.168 - 0.223: 7 0.223 - 0.279: 2 Chirality restraints: 3530 Sorted by residual: chirality pdb=" C3' ANP D1901 " pdb=" C2' ANP D1901 " pdb=" C4' ANP D1901 " pdb=" O3' ANP D1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3527 not shown) Planarity restraints: 4114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 231 " -0.262 9.50e-02 1.11e+02 1.21e-01 1.97e+01 pdb=" NE ARG D 231 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 231 " 0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG D 231 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 231 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.022 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C THR C 89 " 0.076 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE C 90 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 89 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C THR F 89 " 0.076 2.00e-02 2.50e+03 pdb=" O THR F 89 " -0.028 2.00e-02 2.50e+03 pdb=" N PHE F 90 " -0.026 2.00e-02 2.50e+03 ... (remaining 4111 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 10 2.03 - 2.75: 2392 2.75 - 3.47: 33187 3.47 - 4.18: 55737 4.18 - 4.90: 100456 Nonbonded interactions: 191782 Sorted by model distance: nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.313 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.313 3.350 nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.313 3.350 nonbonded pdb=" OE2 GLU C 205 " pdb=" CG2 DTH I 4 " model vdw 1.375 3.460 nonbonded pdb=" CG2 DTH H 4 " pdb=" OE2 GLU G 205 " model vdw 1.375 3.460 ... (remaining 191777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 7 5.21 5 S 148 5.16 5 C 14851 2.51 5 N 3963 2.21 5 O 4389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.770 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.210 Process input model: 59.600 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 : 0.005 0.141 23866 Z= 0.329 Angle : 0.826 18.831 32265 Z= 0.464 Chirality : 0.048 0.279 3530 Planarity : 0.007 0.121 4114 Dihedral : 14.849 126.822 8876 Min Nonbonded Distance : 1.313 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 2837 helix: -1.75 (0.11), residues: 1340 sheet: 0.29 (0.25), residues: 384 loop : 0.32 (0.17), residues: 1113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 2.915 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 outliers start: 2 outliers final: 3 residues processed: 235 average time/residue: 1.7085 time to fit residues: 449.7615 Evaluate side-chains 127 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.3506 time to fit residues: 4.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 4.9990 chunk 216 optimal weight: 0.2980 chunk 119 optimal weight: 0.0270 chunk 73 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 overall best weight: 2.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 354 HIS A 398 ASN A 493 GLN A 775 GLN B 75 GLN C 162 ASN C 280 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS D 398 ASN D 493 GLN D 775 GLN E 75 GLN F 162 ASN F 280 ASN G 162 ASN G 280 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 23866 Z= 0.328 Angle : 0.647 7.756 32265 Z= 0.334 Chirality : 0.044 0.167 3530 Planarity : 0.004 0.078 4114 Dihedral : 9.024 119.593 3208 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 2837 helix: 0.49 (0.14), residues: 1352 sheet: 0.53 (0.26), residues: 390 loop : 0.79 (0.19), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 141 average time/residue: 1.4713 time to fit residues: 238.0540 Evaluate side-chains 125 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 7 average time/residue: 0.8403 time to fit residues: 11.1283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN D 377 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 23866 Z= 0.421 Angle : 0.639 7.943 32265 Z= 0.326 Chirality : 0.044 0.167 3530 Planarity : 0.004 0.074 4114 Dihedral : 8.837 125.867 3208 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2837 helix: 1.12 (0.14), residues: 1331 sheet: 0.46 (0.26), residues: 387 loop : 0.64 (0.19), residues: 1119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 114 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 135 average time/residue: 1.4199 time to fit residues: 222.6449 Evaluate side-chains 124 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 2.942 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 3 average time/residue: 0.3078 time to fit residues: 5.2742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN A 730 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 23866 Z= 0.200 Angle : 0.548 8.125 32265 Z= 0.274 Chirality : 0.041 0.142 3530 Planarity : 0.004 0.075 4114 Dihedral : 8.523 128.175 3208 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.16), residues: 2837 helix: 1.44 (0.15), residues: 1338 sheet: 0.41 (0.26), residues: 391 loop : 0.65 (0.19), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 138 average time/residue: 1.3725 time to fit residues: 220.2247 Evaluate side-chains 127 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 2.827 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 3 average time/residue: 0.2465 time to fit residues: 4.9669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 205 optimal weight: 30.0000 chunk 113 optimal weight: 0.2980 chunk 235 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 247 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 23866 Z= 0.226 Angle : 0.547 8.647 32265 Z= 0.272 Chirality : 0.041 0.139 3530 Planarity : 0.003 0.073 4114 Dihedral : 8.366 127.974 3208 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2837 helix: 1.55 (0.15), residues: 1346 sheet: 0.62 (0.26), residues: 409 loop : 0.62 (0.19), residues: 1082 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 140 average time/residue: 1.4416 time to fit residues: 233.7171 Evaluate side-chains 122 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 2.787 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 2 average time/residue: 0.2793 time to fit residues: 4.6559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 275 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN C 296 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 HIS F 137 GLN F 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.055 23866 Z= 0.510 Angle : 0.665 10.155 32265 Z= 0.333 Chirality : 0.045 0.162 3530 Planarity : 0.004 0.073 4114 Dihedral : 8.538 130.790 3208 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.16), residues: 2837 helix: 1.41 (0.14), residues: 1341 sheet: 0.32 (0.26), residues: 391 loop : 0.42 (0.19), residues: 1105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 133 average time/residue: 1.3567 time to fit residues: 210.1436 Evaluate side-chains 127 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 2.924 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 0.8585 time to fit residues: 8.3742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 201 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 23866 Z= 0.168 Angle : 0.550 10.357 32265 Z= 0.271 Chirality : 0.040 0.133 3530 Planarity : 0.003 0.072 4114 Dihedral : 8.253 132.357 3208 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.16), residues: 2837 helix: 1.60 (0.15), residues: 1344 sheet: 0.58 (0.26), residues: 409 loop : 0.45 (0.19), residues: 1084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 135 average time/residue: 1.3830 time to fit residues: 218.6907 Evaluate side-chains 124 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 2.782 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 1 average time/residue: 0.3642 time to fit residues: 4.3177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 174 optimal weight: 0.3980 chunk 187 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 23866 Z= 0.319 Angle : 0.603 12.034 32265 Z= 0.293 Chirality : 0.042 0.146 3530 Planarity : 0.003 0.065 4114 Dihedral : 8.246 130.367 3208 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.16), residues: 2837 helix: 1.61 (0.15), residues: 1341 sheet: 0.59 (0.26), residues: 415 loop : 0.45 (0.19), residues: 1081 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 125 average time/residue: 1.3739 time to fit residues: 199.6906 Evaluate side-chains 124 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 0.3013 time to fit residues: 4.8067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 231 optimal weight: 0.0980 chunk 242 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 23866 Z= 0.265 Angle : 0.600 13.501 32265 Z= 0.290 Chirality : 0.041 0.142 3530 Planarity : 0.003 0.063 4114 Dihedral : 8.179 130.504 3208 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.16), residues: 2837 helix: 1.61 (0.15), residues: 1341 sheet: 0.61 (0.26), residues: 415 loop : 0.46 (0.19), residues: 1081 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 128 average time/residue: 1.4965 time to fit residues: 226.8767 Evaluate side-chains 125 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 2.958 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 1 average time/residue: 0.4349 time to fit residues: 4.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 188 optimal weight: 0.0970 chunk 283 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 23866 Z= 0.150 Angle : 0.596 13.420 32265 Z= 0.282 Chirality : 0.040 0.132 3530 Planarity : 0.003 0.062 4114 Dihedral : 7.949 127.712 3208 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.16), residues: 2837 helix: 1.65 (0.15), residues: 1345 sheet: 0.67 (0.26), residues: 415 loop : 0.49 (0.19), residues: 1077 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 129 average time/residue: 1.3712 time to fit residues: 206.7025 Evaluate side-chains 125 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 1 average time/residue: 0.3632 time to fit residues: 4.2936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 0.2980 chunk 198 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.057851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038160 restraints weight = 105942.598| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.66 r_work: 0.2879 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work: 0.2859 rms_B_bonded: 3.41 restraints_weight: 0.1250 r_work: 0.2849 rms_B_bonded: 3.43 restraints_weight: 0.0625 r_work: 0.2839 rms_B_bonded: 3.47 restraints_weight: 0.0312 r_work: 0.2829 rms_B_bonded: 3.53 restraints_weight: 0.0156 r_work: 0.2819 rms_B_bonded: 3.60 restraints_weight: 0.0078 r_work: 0.2808 rms_B_bonded: 3.68 restraints_weight: 0.0039 r_work: 0.2797 rms_B_bonded: 3.77 restraints_weight: 0.0020 r_work: 0.2786 rms_B_bonded: 3.88 restraints_weight: 0.0010 r_work: 0.2775 rms_B_bonded: 4.00 restraints_weight: 0.0005 r_work: 0.2764 rms_B_bonded: 4.13 restraints_weight: 0.0002 r_work: 0.2752 rms_B_bonded: 4.27 restraints_weight: 0.0001 r_work: 0.2740 rms_B_bonded: 4.43 restraints_weight: 0.0001 r_work: 0.2728 rms_B_bonded: 4.61 restraints_weight: 0.0000 r_work: 0.2715 rms_B_bonded: 4.79 restraints_weight: 0.0000 r_work: 0.2703 rms_B_bonded: 4.99 restraints_weight: 0.0000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 23866 Z= 0.252 Angle : 0.604 13.764 32265 Z= 0.292 Chirality : 0.041 0.154 3530 Planarity : 0.003 0.064 4114 Dihedral : 7.896 123.936 3208 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.16), residues: 2837 helix: 1.71 (0.15), residues: 1340 sheet: 0.65 (0.26), residues: 418 loop : 0.49 (0.19), residues: 1079 =============================================================================== Job complete usr+sys time: 5485.18 seconds wall clock time: 100 minutes 26.19 seconds (6026.19 seconds total)