Starting phenix.real_space_refine (version: dev) on Fri May 13 18:46:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1k_8956/05_2022/6e1k_8956_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1k_8956/05_2022/6e1k_8956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1k_8956/05_2022/6e1k_8956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1k_8956/05_2022/6e1k_8956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1k_8956/05_2022/6e1k_8956_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1k_8956/05_2022/6e1k_8956_neut_updated.pdb" } resolution = 3.3 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= 1.000 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 ARG 62": "NH1" <-> "NH2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 98": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 11641 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4278 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 519} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4278 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 519} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 539 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 75, 539 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 541 Chain: "D" Number of atoms: 870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 887 Chain: "E" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 539 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 75, 539 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 541 Chain: "F" Number of atoms: 870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 887 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'PLM': 8, ' CA': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 111 Unusual residues: {'PLM': 6, ' CA': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.01, per 1000 atoms: 0.69 Number of scatterers: 11641 At special positions: 0 Unit cell: (114.266, 115.482, 109.404, 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) Ca 7 19.99 S 52 16.00 P 6 15.00 O 2144 8.00 N 1780 7.00 C 7652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.91 Conformation dependent library (CDL) restraints added in 2.1 seconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 7 sheets defined 41.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 No H-bonds generated for 'chain 'A' and resid 37 through 40' Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.521A pdb=" N PHE A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 69' Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.957A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 154 through 172 removed outlier: 3.792A pdb=" N VAL A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.524A pdb=" N VAL A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 237 removed outlier: 3.909A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 252 through 262 removed outlier: 4.216A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.135A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.581A pdb=" N SER A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 287 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A 288 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 removed outlier: 4.297A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 323 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 331 through 334 No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 344 through 354 removed outlier: 4.330A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.874A pdb=" N LYS A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.947A pdb=" N ASP A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 removed outlier: 3.735A pdb=" N THR A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 576 through 586 removed outlier: 4.234A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 616 through 628 removed outlier: 4.128A pdb=" N VAL A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 642 removed outlier: 3.709A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 665 removed outlier: 3.786A pdb=" N VAL A 653 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 654 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE A 655 " --> pdb=" O PHE A 652 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 657 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 658 " --> pdb=" O PHE A 655 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU A 662 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU A 663 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN A 665 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 675 removed outlier: 3.552A pdb=" N GLU A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 691 removed outlier: 4.386A pdb=" N GLU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.628A pdb=" N ASP B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 66 through 69 No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.555A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 153 through 172 removed outlier: 3.646A pdb=" N VAL B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 removed outlier: 3.509A pdb=" N PHE B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.854A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 237 removed outlier: 3.916A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 4.176A pdb=" N GLN B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 4.140A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 271' Processing helix chain 'B' and resid 279 through 294 removed outlier: 3.711A pdb=" N PHE B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 286 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 287 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR B 288 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 289 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 292 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 293 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 294 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 329 removed outlier: 4.292A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 326 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 344 through 354 removed outlier: 3.736A pdb=" N GLU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 4.383A pdb=" N LYS B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 391 removed outlier: 3.642A pdb=" N ASP B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 398 No H-bonds generated for 'chain 'B' and resid 395 through 398' Processing helix chain 'B' and resid 552 through 565 removed outlier: 3.733A pdb=" N THR B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 576 through 586 removed outlier: 4.204A pdb=" N SER B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 No H-bonds generated for 'chain 'B' and resid 602 through 605' Processing helix chain 'B' and resid 616 through 628 removed outlier: 4.107A pdb=" N VAL B 621 " --> pdb=" O PRO B 617 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 642 removed outlier: 3.741A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.540A pdb=" N TYR B 651 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 653 " --> pdb=" O THR B 650 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 654 " --> pdb=" O TYR B 651 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE B 655 " --> pdb=" O PHE B 652 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 658 " --> pdb=" O PHE B 655 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 659 " --> pdb=" O TYR B 656 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 660 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 662 " --> pdb=" O THR B 659 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU B 663 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN B 665 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 Processing helix chain 'B' and resid 680 through 690 removed outlier: 4.440A pdb=" N GLU B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 706 removed outlier: 4.011A pdb=" N LYS B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing sheet with id= A, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.684A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 35 through 37 removed outlier: 5.760A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 5 through 7 Processing sheet with id= D, first strand: chain 'D' and resid 35 through 38 removed outlier: 6.183A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 21 through 24 removed outlier: 3.592A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 5 through 7 Processing sheet with id= G, first strand: chain 'F' and resid 35 through 38 removed outlier: 6.187A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1898 1.31 - 1.43: 3404 1.43 - 1.56: 6484 1.56 - 1.68: 28 1.68 - 1.81: 78 Bond restraints: 11892 Sorted by residual: bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CA SER C 91 " pdb=" CB SER C 91 " ideal model delta sigma weight residual 1.532 1.468 0.063 1.45e-02 4.76e+03 1.92e+01 ... (remaining 11887 not shown) Histogram of bond angle deviations from ideal: 91.21 - 103.00: 91 103.00 - 114.78: 7023 114.78 - 126.57: 8806 126.57 - 138.35: 176 138.35 - 150.14: 2 Bond angle restraints: 16098 Sorted by residual: angle pdb=" CA LEU E 73 " pdb=" CB LEU E 73 " pdb=" CG LEU E 73 " ideal model delta sigma weight residual 116.30 150.14 -33.84 3.50e+00 8.16e-02 9.35e+01 angle pdb=" CA LEU C 73 " pdb=" CB LEU C 73 " pdb=" CG LEU C 73 " ideal model delta sigma weight residual 116.30 149.60 -33.30 3.50e+00 8.16e-02 9.05e+01 angle pdb=" N LEU A 610 " pdb=" CA LEU A 610 " pdb=" C LEU A 610 " ideal model delta sigma weight residual 110.80 91.21 19.59 2.13e+00 2.20e-01 8.46e+01 angle pdb=" C LEU A 609 " pdb=" N LEU A 610 " pdb=" CA LEU A 610 " ideal model delta sigma weight residual 121.54 135.37 -13.83 1.91e+00 2.74e-01 5.24e+01 angle pdb=" C VAL D 29 " pdb=" N TYR D 30 " pdb=" CA TYR D 30 " ideal model delta sigma weight residual 121.54 133.55 -12.01 1.91e+00 2.74e-01 3.96e+01 ... (remaining 16093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6406 17.94 - 35.89: 426 35.89 - 53.83: 74 53.83 - 71.77: 35 71.77 - 89.71: 5 Dihedral angle restraints: 6946 sinusoidal: 2688 harmonic: 4258 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual -86.00 -175.71 89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual -86.00 -175.26 89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LEU B 661 " pdb=" CA LEU B 661 " ideal model delta harmonic sigma weight residual 180.00 133.93 46.07 0 5.00e+00 4.00e-02 8.49e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1472 0.101 - 0.201: 293 0.201 - 0.302: 39 0.302 - 0.402: 5 0.402 - 0.502: 3 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CB THR D 107 " pdb=" CA THR D 107 " pdb=" OG1 THR D 107 " pdb=" CG2 THR D 107 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 1809 not shown) Planarity restraints: 1972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 107 " -0.050 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR A 107 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 107 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 107 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 107 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 107 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 107 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 107 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 107 " 0.044 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR B 107 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 107 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 107 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 107 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 107 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 107 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 107 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 36 " -0.046 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR E 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR E 36 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR E 36 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR E 36 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR E 36 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 36 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 36 " -0.031 2.00e-02 2.50e+03 ... (remaining 1969 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 231 2.62 - 3.19: 10110 3.19 - 3.76: 17801 3.76 - 4.33: 25320 4.33 - 4.90: 40145 Nonbonded interactions: 93607 Sorted by model distance: nonbonded pdb=" OH TYR A 114 " pdb=" OD2 ASP A 615 " model vdw 2.047 2.440 nonbonded pdb=" OD2 ASP B 606 " pdb=" O HOH B 901 " model vdw 2.080 2.440 nonbonded pdb=" OD2 ASP A 606 " pdb=" O HOH A 901 " model vdw 2.095 2.440 nonbonded pdb=" N LEU A 610 " pdb=" O LEU A 610 " model vdw 2.099 2.496 nonbonded pdb=" O THR D 105 " pdb=" OG1 THR D 105 " model vdw 2.124 2.440 ... (remaining 93602 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' and (resid 22 through 707 or resid 801 through 803 or resid 805 throu \ gh 809)) selection = (chain 'B' and (resid 22 through 707 or resid 801 through 803 or resid 805 throu \ gh 809)) } ncs_group { reference = (chain 'C' and (resid 4 through 64 or resid 66 through 100)) selection = (chain 'E' and (resid 4 through 64 or resid 66 through 100)) } ncs_group { reference = (chain 'D' and (resid 2 through 16 or resid 18 through 120)) selection = (chain 'F' and (resid 2 through 16 or resid 18 through 120)) } 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 Ca 7 9.91 5 P 6 5.49 5 S 52 5.16 5 C 7652 2.51 5 N 1780 2.21 5 O 2144 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=0.30 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.780 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.110 Process input model: 34.040 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 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 : 0.019 0.180 11892 Z= 1.187 Angle : 1.757 33.840 16098 Z= 0.882 Chirality : 0.084 0.502 1812 Planarity : 0.009 0.076 1972 Dihedral : 13.485 75.250 4198 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.39 % Favored : 88.32 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 1.14 % 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: -6.12 (0.15), residues: 1400 helix: -4.20 (0.10), residues: 684 sheet: -4.08 (0.31), residues: 152 loop : -3.62 (0.21), residues: 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 262 average time/residue: 0.2561 time to fit residues: 93.6016 Evaluate side-chains 162 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1058 time to fit residues: 3.2519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 0.0980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 257 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 11892 Z= 0.218 Angle : 0.722 10.622 16098 Z= 0.374 Chirality : 0.043 0.201 1812 Planarity : 0.006 0.098 1972 Dihedral : 12.085 59.882 1776 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -4.90 (0.18), residues: 1400 helix: -3.14 (0.14), residues: 684 sheet: -3.59 (0.36), residues: 144 loop : -3.08 (0.23), residues: 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 202 average time/residue: 0.2235 time to fit residues: 65.8719 Evaluate side-chains 158 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1111 time to fit residues: 2.4511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 103 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11892 Z= 0.196 Angle : 0.654 8.801 16098 Z= 0.334 Chirality : 0.041 0.163 1812 Planarity : 0.005 0.105 1972 Dihedral : 11.105 59.790 1776 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.00 (0.20), residues: 1400 helix: -2.44 (0.16), residues: 700 sheet: -2.99 (0.40), residues: 144 loop : -2.62 (0.25), residues: 556 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 189 average time/residue: 0.2142 time to fit residues: 59.4764 Evaluate side-chains 158 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1047 time to fit residues: 2.5703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 129 optimal weight: 0.3980 chunk 137 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN D 28 ASN F 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11892 Z= 0.163 Angle : 0.597 8.082 16098 Z= 0.306 Chirality : 0.040 0.143 1812 Planarity : 0.004 0.105 1972 Dihedral : 10.308 59.647 1776 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.21), residues: 1400 helix: -1.80 (0.18), residues: 694 sheet: -2.58 (0.42), residues: 152 loop : -2.52 (0.25), residues: 554 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 189 average time/residue: 0.2001 time to fit residues: 57.5859 Evaluate side-chains 166 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1132 time to fit residues: 2.8387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 11892 Z= 0.205 Angle : 0.632 11.967 16098 Z= 0.320 Chirality : 0.041 0.139 1812 Planarity : 0.004 0.108 1972 Dihedral : 10.323 59.496 1776 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.22), residues: 1400 helix: -1.46 (0.18), residues: 696 sheet: -2.34 (0.43), residues: 150 loop : -2.35 (0.26), residues: 554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 179 average time/residue: 0.2109 time to fit residues: 56.2151 Evaluate side-chains 163 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1080 time to fit residues: 3.7138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.0470 chunk 137 optimal weight: 0.0000 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN F 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11892 Z= 0.168 Angle : 0.606 9.492 16098 Z= 0.303 Chirality : 0.040 0.142 1812 Planarity : 0.004 0.073 1972 Dihedral : 9.796 59.473 1776 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.22), residues: 1400 helix: -1.18 (0.19), residues: 696 sheet: -2.14 (0.43), residues: 152 loop : -2.23 (0.26), residues: 552 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 168 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 172 average time/residue: 0.2053 time to fit residues: 53.6536 Evaluate side-chains 160 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 154 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1255 time to fit residues: 3.1873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN D 28 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11892 Z= 0.208 Angle : 0.629 9.299 16098 Z= 0.312 Chirality : 0.042 0.272 1812 Planarity : 0.003 0.059 1972 Dihedral : 9.773 59.560 1776 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.22), residues: 1400 helix: -0.98 (0.19), residues: 698 sheet: -1.94 (0.44), residues: 148 loop : -2.24 (0.26), residues: 554 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 169 average time/residue: 0.2020 time to fit residues: 52.2600 Evaluate side-chains 157 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1043 time to fit residues: 2.6113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 124 optimal weight: 0.0670 chunk 131 optimal weight: 7.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11892 Z= 0.197 Angle : 0.626 8.824 16098 Z= 0.310 Chirality : 0.041 0.200 1812 Planarity : 0.003 0.052 1972 Dihedral : 9.507 59.528 1776 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 1.17 % 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: -2.31 (0.22), residues: 1400 helix: -0.83 (0.19), residues: 706 sheet: -1.85 (0.45), residues: 148 loop : -2.28 (0.26), residues: 546 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 161 average time/residue: 0.1895 time to fit residues: 46.5525 Evaluate side-chains 159 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1326 time to fit residues: 3.1749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 115 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 11892 Z= 0.225 Angle : 0.636 8.669 16098 Z= 0.315 Chirality : 0.042 0.162 1812 Planarity : 0.003 0.049 1972 Dihedral : 9.486 59.681 1776 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1400 helix: -0.70 (0.19), residues: 708 sheet: -1.85 (0.44), residues: 148 loop : -2.25 (0.26), residues: 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 155 average time/residue: 0.2002 time to fit residues: 47.4099 Evaluate side-chains 153 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1060 time to fit residues: 1.9546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 141 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 0.0470 chunk 89 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 11892 Z= 0.200 Angle : 0.617 8.630 16098 Z= 0.304 Chirality : 0.041 0.150 1812 Planarity : 0.003 0.047 1972 Dihedral : 9.169 58.486 1776 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1400 helix: -0.50 (0.20), residues: 704 sheet: -1.73 (0.44), residues: 150 loop : -2.13 (0.26), residues: 546 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 152 average time/residue: 0.2003 time to fit residues: 46.9178 Evaluate side-chains 152 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1350 time to fit residues: 2.4893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.261253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.224590 restraints weight = 31784.633| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 6.15 r_work: 0.4472 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4855 r_free = 0.4855 target_work(ls_wunit_k1) = 0.261 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4855 r_free = 0.4855 target_work(ls_wunit_k1) = 0.261 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 11892 Z= 0.219 Angle : 0.638 9.250 16098 Z= 0.313 Chirality : 0.042 0.162 1812 Planarity : 0.003 0.046 1972 Dihedral : 9.276 59.900 1776 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.22), residues: 1400 helix: -0.51 (0.19), residues: 710 sheet: -1.75 (0.44), residues: 148 loop : -2.17 (0.26), residues: 542 =============================================================================== Job complete usr+sys time: 2098.40 seconds wall clock time: 39 minutes 13.36 seconds (2353.36 seconds total)