Starting phenix.real_space_refine on Thu Apr 11 00:24:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/04_2024/7lp9_23473_neut_updated.pdb" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 112 5.16 5 Na 2 4.78 5 C 13765 2.51 5 N 3224 2.21 5 O 3838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C GLU 651": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D GLU 651": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20977 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4906 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 616} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4906 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 616} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 119 Chain: "C" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4906 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 616} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4906 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 616} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 119 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 309 Unusual residues: {' NA': 2, '6OU': 7, 'LBN': 2, 'T7X': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 335 Unusual residues: {'6OU': 7, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 369 Unusual residues: {'6OU': 7, 'LBN': 2, 'T7X': 1, 'YFP': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'YFP:plan-3': 2, 'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 340 Unusual residues: {'6OU': 7, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 39 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA D 204 " occ=0.50 Time building chain proxies: 11.50, per 1000 atoms: 0.55 Number of scatterers: 20977 At special positions: 0 Unit cell: (134.875, 134.875, 121.927, 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 112 16.00 P 36 15.00 Na 2 11.00 O 3838 8.00 N 3224 7.00 C 13765 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: 9.50 Conformation dependent library (CDL) restraints added in 3.9 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 8 sheets defined 55.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 128 through 139 removed outlier: 4.284A pdb=" N LEU A 133 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 171 through 182 Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 558 removed outlier: 3.814A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.995A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.849A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 690 through 711 removed outlier: 4.077A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 128 through 139 removed outlier: 4.312A pdb=" N LEU B 133 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 171 through 182 Processing helix chain 'B' and resid 186 through 189 No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 558 removed outlier: 3.826A pdb=" N VAL B 538 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.961A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.849A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 711 removed outlier: 4.076A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 128 through 139 removed outlier: 4.280A pdb=" N LEU C 133 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 186 through 189 No H-bonds generated for 'chain 'C' and resid 186 through 189' Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 558 removed outlier: 3.825A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 4.002A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.849A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 711 removed outlier: 4.074A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 128 through 139 removed outlier: 4.282A pdb=" N LEU D 133 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 186 through 189 No H-bonds generated for 'chain 'D' and resid 186 through 189' Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 558 removed outlier: 3.828A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 4.001A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.848A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 690 through 711 removed outlier: 4.078A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 6.643A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 724 through 730 removed outlier: 6.959A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 6.639A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 724 through 730 removed outlier: 6.953A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.502A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 724 through 730 removed outlier: 6.959A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 742 through 747 removed outlier: 3.513A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 724 through 730 removed outlier: 6.958A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) 1007 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 10.00 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: 3164 1.31 - 1.43: 5884 1.43 - 1.56: 11777 1.56 - 1.68: 330 1.68 - 1.81: 232 Bond restraints: 21387 Sorted by residual: bond pdb=" O2 LBN C 902 " pdb=" P1 LBN C 902 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" O2 LBN A 910 " pdb=" P1 LBN A 910 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O2 LBN D 903 " pdb=" P1 LBN D 903 " ideal model delta sigma weight residual 1.650 1.790 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O2 LBN B 902 " pdb=" P1 LBN B 902 " ideal model delta sigma weight residual 1.650 1.790 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O2 LBN D 905 " pdb=" P1 LBN D 905 " ideal model delta sigma weight residual 1.650 1.788 -0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 21382 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.81: 338 105.81 - 112.86: 11199 112.86 - 119.91: 7473 119.91 - 126.96: 9641 126.96 - 134.01: 191 Bond angle restraints: 28842 Sorted by residual: angle pdb=" CG1 VAL C 430 " pdb=" CB VAL C 430 " pdb=" CG2 VAL C 430 " ideal model delta sigma weight residual 110.80 122.35 -11.55 2.20e+00 2.07e-01 2.75e+01 angle pdb=" CG1 VAL B 430 " pdb=" CB VAL B 430 " pdb=" CG2 VAL B 430 " ideal model delta sigma weight residual 110.80 122.34 -11.54 2.20e+00 2.07e-01 2.75e+01 angle pdb=" CG1 VAL D 430 " pdb=" CB VAL D 430 " pdb=" CG2 VAL D 430 " ideal model delta sigma weight residual 110.80 122.32 -11.52 2.20e+00 2.07e-01 2.74e+01 angle pdb=" CG1 VAL A 430 " pdb=" CB VAL A 430 " pdb=" CG2 VAL A 430 " ideal model delta sigma weight residual 110.80 122.29 -11.49 2.20e+00 2.07e-01 2.73e+01 angle pdb=" O1 T7X C 904 " pdb=" P1 T7X C 904 " pdb=" O13 T7X C 904 " ideal model delta sigma weight residual 94.60 109.69 -15.09 3.00e+00 1.11e-01 2.53e+01 ... (remaining 28837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 12276 34.51 - 69.01: 493 69.01 - 103.52: 82 103.52 - 138.03: 45 138.03 - 172.54: 24 Dihedral angle restraints: 12920 sinusoidal: 5476 harmonic: 7444 Sorted by residual: dihedral pdb=" C19 6OU A 903 " pdb=" C20 6OU A 903 " pdb=" C21 6OU A 903 " pdb=" O22 6OU A 903 " ideal model delta sinusoidal sigma weight residual -59.00 113.54 -172.54 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C19 6OU D 906 " pdb=" C20 6OU D 906 " pdb=" C21 6OU D 906 " pdb=" O22 6OU D 906 " ideal model delta sinusoidal sigma weight residual -59.00 113.49 -172.49 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C19 6OU B 906 " pdb=" C20 6OU B 906 " pdb=" C21 6OU B 906 " pdb=" O22 6OU B 906 " ideal model delta sinusoidal sigma weight residual -59.00 113.32 -172.32 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 3211 0.965 - 1.931: 8 1.931 - 2.896: 0 2.896 - 3.861: 0 3.861 - 4.827: 4 Chirality restraints: 3223 Sorted by residual: chirality pdb=" C1 T7X B 904 " pdb=" C2 T7X B 904 " pdb=" C6 T7X B 904 " pdb=" O1 T7X B 904 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 T7X C 904 " pdb=" C2 T7X C 904 " pdb=" C6 T7X C 904 " pdb=" O1 T7X C 904 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 T7X A 901 " pdb=" C2 T7X A 901 " pdb=" C6 T7X A 901 " pdb=" O1 T7X A 901 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.82e+02 ... (remaining 3220 not shown) Planarity restraints: 3516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 653 " -0.010 2.00e-02 2.50e+03 1.15e-02 2.66e+00 pdb=" CG TYR A 653 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 653 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 653 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 653 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 653 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 653 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 653 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 653 " -0.011 2.00e-02 2.50e+03 1.14e-02 2.60e+00 pdb=" CG TYR B 653 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 653 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 653 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 653 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 653 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 653 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 653 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 304 " 0.018 2.00e-02 2.50e+03 1.22e-02 2.59e+00 pdb=" CG PHE D 304 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE D 304 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 304 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 304 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 304 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 304 " 0.008 2.00e-02 2.50e+03 ... (remaining 3513 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 184 2.61 - 3.18: 18609 3.18 - 3.76: 30558 3.76 - 4.33: 43928 4.33 - 4.90: 73820 Nonbonded interactions: 167099 Sorted by model distance: nonbonded pdb=" OD1 ASP C 383 " pdb=" OG SER C 385 " model vdw 2.040 2.440 nonbonded pdb=" OD1 ASP B 383 " pdb=" OG SER B 385 " model vdw 2.040 2.440 nonbonded pdb=" OD1 ASP D 383 " pdb=" OG SER D 385 " model vdw 2.042 2.440 nonbonded pdb=" OD1 ASP A 383 " pdb=" OG SER A 385 " model vdw 2.043 2.440 nonbonded pdb=" NH1 ARG A 355 " pdb=" O LEU A 365 " model vdw 2.099 2.520 ... (remaining 167094 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 113 through 766 or (resid 906 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37)) or ( \ resid 907 and (name C40 or name C41 or name C42 or name C43)) or (resid 909 and \ (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 9 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name O17 or name O18 or name O30 or name O32)))) selection = (chain 'B' and (resid 113 through 766 or (resid 906 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37)) or ( \ resid 907 and (name C40 or name C41 or name C42 or name C43)) or (resid 909 and \ (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 9 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name O17 or name O18 or name O30 or name O32)))) selection = (chain 'C' and (resid 113 through 766 or (resid 906 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37)) or ( \ resid 907 and (name C40 or name C41 or name C42 or name C43)) or (resid 909 and \ (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 9 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name O17 or name O18 or name O30 or name O32)))) selection = (chain 'D' and (resid 113 through 766 or (resid 906 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37)) or ( \ resid 907 and (name C40 or name C41 or name C42 or name C43)) or (resid 909 and \ (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 9 or name C20 or name C21 or name C31 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name O17 or name O18 or name O30 or name O32)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.500 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: 4.960 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 57.700 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.141 21387 Z= 0.637 Angle : 1.069 15.095 28842 Z= 0.424 Chirality : 0.196 4.827 3223 Planarity : 0.002 0.030 3516 Dihedral : 22.019 172.536 8128 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.57 (0.17), residues: 2520 helix: 2.23 (0.13), residues: 1524 sheet: -1.15 (0.38), residues: 116 loop : -0.79 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 697 HIS 0.003 0.001 HIS D 378 PHE 0.025 0.001 PHE A 304 TYR 0.026 0.001 TYR A 653 ARG 0.002 0.000 ARG C 579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.375 Fit side-chains REVERT: A 562 MET cc_start: 0.8807 (mmm) cc_final: 0.8607 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.2366 time to fit residues: 175.1856 Evaluate side-chains 114 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 7.9990 chunk 191 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 50.0000 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 378 HIS A 700 GLN ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 378 HIS B 700 GLN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 378 HIS C 700 GLN ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN D 378 HIS D 700 GLN ** D 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21387 Z= 0.194 Angle : 0.503 7.777 28842 Z= 0.259 Chirality : 0.039 0.325 3223 Planarity : 0.004 0.027 3516 Dihedral : 21.204 172.557 3932 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.99 % Allowed : 2.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.57 (0.17), residues: 2520 helix: 2.13 (0.13), residues: 1508 sheet: -0.81 (0.45), residues: 84 loop : -0.61 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 697 HIS 0.002 0.000 HIS D 289 PHE 0.010 0.001 PHE C 429 TYR 0.011 0.001 TYR D 194 ARG 0.001 0.000 ARG C 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 2.313 Fit side-chains REVERT: A 562 MET cc_start: 0.8852 (mmm) cc_final: 0.8567 (mmm) outliers start: 20 outliers final: 4 residues processed: 121 average time/residue: 1.2527 time to fit residues: 175.7128 Evaluate side-chains 116 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 190 optimal weight: 50.0000 chunk 155 optimal weight: 0.0040 chunk 63 optimal weight: 30.0000 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21387 Z= 0.250 Angle : 0.489 6.102 28842 Z= 0.255 Chirality : 0.039 0.248 3223 Planarity : 0.003 0.030 3516 Dihedral : 19.579 178.062 3932 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.19 % Allowed : 5.67 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.37 (0.17), residues: 2520 helix: 2.03 (0.13), residues: 1500 sheet: -0.69 (0.45), residues: 84 loop : -0.81 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 697 HIS 0.002 0.000 HIS C 289 PHE 0.010 0.001 PHE C 649 TYR 0.010 0.001 TYR C 194 ARG 0.002 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 2.381 Fit side-chains REVERT: A 214 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7889 (tpt) REVERT: A 304 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7720 (t80) REVERT: A 562 MET cc_start: 0.8913 (mmm) cc_final: 0.8666 (mmm) REVERT: B 304 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7762 (t80) REVERT: D 214 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7899 (tpt) REVERT: D 304 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7765 (t80) outliers start: 24 outliers final: 10 residues processed: 113 average time/residue: 1.2568 time to fit residues: 164.8277 Evaluate side-chains 116 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 153 optimal weight: 0.0170 chunk 230 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 748 ASN B 378 HIS B 676 ASN B 748 ASN C 378 HIS C 748 ASN D 378 HIS D 748 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21387 Z= 0.118 Angle : 0.417 5.730 28842 Z= 0.220 Chirality : 0.035 0.131 3223 Planarity : 0.003 0.029 3516 Dihedral : 17.798 177.633 3932 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.64 % Allowed : 6.36 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.63 (0.17), residues: 2520 helix: 2.25 (0.13), residues: 1468 sheet: -0.64 (0.48), residues: 84 loop : -0.61 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 697 HIS 0.001 0.000 HIS A 289 PHE 0.008 0.001 PHE A 659 TYR 0.007 0.001 TYR B 194 ARG 0.001 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 2.531 Fit side-chains REVERT: A 214 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7904 (tpt) REVERT: A 304 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 304 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.8103 (t80) REVERT: D 214 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7908 (tpt) REVERT: D 304 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.8113 (t80) outliers start: 33 outliers final: 0 residues processed: 118 average time/residue: 1.1383 time to fit residues: 158.0747 Evaluate side-chains 110 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 304 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 2.9990 chunk 138 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 207 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 218 optimal weight: 0.0020 chunk 61 optimal weight: 7.9990 overall best weight: 1.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 676 ASN B 378 HIS C 378 HIS C 676 ASN D 378 HIS D 676 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21387 Z= 0.179 Angle : 0.433 5.700 28842 Z= 0.226 Chirality : 0.036 0.153 3223 Planarity : 0.003 0.028 3516 Dihedral : 17.172 172.503 3932 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.09 % Allowed : 7.60 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.17), residues: 2520 helix: 2.10 (0.13), residues: 1496 sheet: -0.59 (0.49), residues: 84 loop : -0.56 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 697 HIS 0.002 0.000 HIS C 289 PHE 0.008 0.001 PHE D 649 TYR 0.007 0.001 TYR D 194 ARG 0.001 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 2.576 Fit side-chains REVERT: A 214 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7902 (tpt) REVERT: A 562 MET cc_start: 0.8871 (mmm) cc_final: 0.8635 (mmp) REVERT: D 214 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7915 (tpt) outliers start: 22 outliers final: 7 residues processed: 116 average time/residue: 1.2189 time to fit residues: 164.7219 Evaluate side-chains 110 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 304 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.5980 chunk 219 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS C 378 HIS C 676 ASN D 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21387 Z= 0.144 Angle : 0.413 6.029 28842 Z= 0.216 Chirality : 0.035 0.131 3223 Planarity : 0.003 0.028 3516 Dihedral : 16.372 166.625 3932 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.14 % Allowed : 8.10 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.62 (0.17), residues: 2520 helix: 2.17 (0.13), residues: 1484 sheet: -0.54 (0.51), residues: 84 loop : -0.54 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 697 HIS 0.001 0.000 HIS A 289 PHE 0.007 0.001 PHE B 659 TYR 0.006 0.001 TYR B 194 ARG 0.002 0.000 ARG C 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 2.351 Fit side-chains REVERT: A 445 MET cc_start: 0.9119 (tpp) cc_final: 0.8912 (mmm) REVERT: B 445 MET cc_start: 0.9119 (tpp) cc_final: 0.8913 (mmm) REVERT: C 445 MET cc_start: 0.9115 (tpp) cc_final: 0.8908 (mmm) REVERT: D 445 MET cc_start: 0.9116 (tpp) cc_final: 0.8909 (mmm) outliers start: 23 outliers final: 7 residues processed: 110 average time/residue: 1.2480 time to fit residues: 159.4118 Evaluate side-chains 108 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain D residue 304 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 0.0070 chunk 178 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 242 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS B 378 HIS C 378 HIS D 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21387 Z= 0.212 Angle : 0.445 5.558 28842 Z= 0.232 Chirality : 0.036 0.155 3223 Planarity : 0.003 0.028 3516 Dihedral : 16.191 161.361 3932 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.24 % Allowed : 7.95 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.59 (0.17), residues: 2520 helix: 2.10 (0.13), residues: 1476 sheet: -0.54 (0.50), residues: 84 loop : -0.43 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 697 HIS 0.002 0.000 HIS A 289 PHE 0.009 0.001 PHE C 649 TYR 0.008 0.001 TYR C 555 ARG 0.002 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 2.533 Fit side-chains REVERT: A 562 MET cc_start: 0.8890 (mmm) cc_final: 0.8633 (mmm) REVERT: A 720 PHE cc_start: 0.7529 (m-80) cc_final: 0.7262 (m-80) REVERT: C 478 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8200 (mt-10) outliers start: 25 outliers final: 11 residues processed: 115 average time/residue: 1.2984 time to fit residues: 173.3030 Evaluate side-chains 113 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 758 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 50.0000 chunk 220 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS B 378 HIS C 378 HIS C 676 ASN D 378 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21387 Z= 0.129 Angle : 0.412 6.430 28842 Z= 0.214 Chirality : 0.035 0.123 3223 Planarity : 0.003 0.029 3516 Dihedral : 15.063 156.376 3932 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.19 % Allowed : 8.45 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.66 (0.17), residues: 2520 helix: 2.18 (0.14), residues: 1468 sheet: -0.49 (0.51), residues: 84 loop : -0.44 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 697 HIS 0.001 0.000 HIS A 289 PHE 0.007 0.001 PHE D 659 TYR 0.006 0.001 TYR C 555 ARG 0.001 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 2.469 Fit side-chains REVERT: A 720 PHE cc_start: 0.7549 (m-80) cc_final: 0.7256 (m-80) outliers start: 24 outliers final: 11 residues processed: 114 average time/residue: 1.1785 time to fit residues: 156.9984 Evaluate side-chains 111 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 758 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 204 optimal weight: 0.0470 chunk 214 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS B 378 HIS C 676 ASN D 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 21387 Z= 0.122 Angle : 0.407 6.812 28842 Z= 0.211 Chirality : 0.035 0.128 3223 Planarity : 0.003 0.029 3516 Dihedral : 14.334 150.218 3932 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.24 % Allowed : 8.45 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.17), residues: 2520 helix: 2.08 (0.14), residues: 1492 sheet: -0.74 (0.43), residues: 116 loop : -0.53 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 697 HIS 0.003 0.000 HIS C 378 PHE 0.007 0.001 PHE D 659 TYR 0.006 0.001 TYR C 309 ARG 0.002 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 2.445 Fit side-chains REVERT: A 304 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8040 (t80) REVERT: A 720 PHE cc_start: 0.7633 (m-80) cc_final: 0.7362 (m-80) REVERT: B 304 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8052 (t80) REVERT: B 720 PHE cc_start: 0.7543 (m-80) cc_final: 0.7273 (m-80) REVERT: D 304 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8075 (t80) outliers start: 25 outliers final: 8 residues processed: 118 average time/residue: 1.1245 time to fit residues: 156.3357 Evaluate side-chains 110 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 758 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 251 optimal weight: 0.4980 chunk 231 optimal weight: 0.0010 chunk 199 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS B 378 HIS C 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21387 Z= 0.118 Angle : 0.406 7.054 28842 Z= 0.209 Chirality : 0.035 0.131 3223 Planarity : 0.003 0.029 3516 Dihedral : 14.007 147.033 3932 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.70 % Allowed : 9.15 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.55 (0.17), residues: 2520 helix: 2.08 (0.14), residues: 1492 sheet: -0.68 (0.43), residues: 116 loop : -0.51 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.001 0.000 HIS D 289 PHE 0.007 0.001 PHE C 659 TYR 0.006 0.001 TYR C 309 ARG 0.001 0.000 ARG D 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 2.490 Fit side-chains REVERT: A 304 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8085 (t80) REVERT: A 720 PHE cc_start: 0.7615 (m-80) cc_final: 0.7305 (m-80) REVERT: B 304 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8083 (t80) REVERT: B 720 PHE cc_start: 0.7579 (m-80) cc_final: 0.7277 (m-80) REVERT: D 304 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.8123 (t80) outliers start: 14 outliers final: 7 residues processed: 114 average time/residue: 1.1452 time to fit residues: 153.5931 Evaluate side-chains 109 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 758 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 700 GLN B 378 HIS ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.063518 restraints weight = 39477.724| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.52 r_work: 0.2699 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21387 Z= 0.349 Angle : 0.549 16.760 28842 Z= 0.273 Chirality : 0.039 0.184 3223 Planarity : 0.003 0.028 3516 Dihedral : 15.108 146.281 3932 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.80 % Allowed : 9.19 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.40 (0.17), residues: 2520 helix: 1.93 (0.14), residues: 1476 sheet: -0.67 (0.42), residues: 116 loop : -0.48 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.002 0.001 HIS B 289 PHE 0.012 0.001 PHE B 649 TYR 0.011 0.001 TYR B 194 ARG 0.004 0.000 ARG D 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.98 seconds wall clock time: 87 minutes 34.95 seconds (5254.95 seconds total)