Starting phenix.real_space_refine on Tue Dec 12 10:23:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/12_2023/7lp9_23473_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/12_2023/7lp9_23473.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/12_2023/7lp9_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_23473/12_2023/7lp9_23473_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/12_2023/7lp9_23473_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/12_2023/7lp9_23473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/12_2023/7lp9_23473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/12_2023/7lp9_23473_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lp9_23473/12_2023/7lp9_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-1.21rc1-5172/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: 11.17, per 1000 atoms: 0.53 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: 8.66 Conformation dependent library (CDL) restraints added in 3.8 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: 4.40 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: 6.45 Time building geometry restraints manager: 9.25 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.700 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 56.670 Find NCS groups from input model: 1.620 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.470 ------------------------------------------------------------------------------- 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 : 2.458 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.1377 time to fit residues: 162.6395 Evaluate side-chains 114 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.378 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1159 ------------------------------------------------------------------------------- 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: 0.8252 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21387 Z= 0.196 Angle : 0.506 7.966 28842 Z= 0.259 Chirality : 0.039 0.309 3223 Planarity : 0.004 0.027 3516 Dihedral : 21.098 172.936 3932 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.99 % Allowed : 2.53 % Favored : 96.47 % 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: 1.58 (0.17), residues: 2520 helix: 2.14 (0.13), residues: 1508 sheet: -0.80 (0.45), residues: 84 loop : -0.60 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 697 HIS 0.002 0.000 HIS D 289 PHE 0.010 0.001 PHE C 429 TYR 0.011 0.001 TYR A 653 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 139 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 2.175 Fit side-chains outliers start: 20 outliers final: 4 residues processed: 120 average time/residue: 1.2418 time to fit residues: 173.5209 Evaluate side-chains 117 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.6938 time to fit residues: 11.4393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 190 optimal weight: 50.0000 chunk 155 optimal weight: 1.9990 chunk 63 optimal weight: 40.0000 chunk 229 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** D 765 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21387 Z= 0.308 Angle : 0.520 6.531 28842 Z= 0.271 Chirality : 0.040 0.262 3223 Planarity : 0.004 0.031 3516 Dihedral : 19.732 179.173 3932 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.34 % Allowed : 5.72 % Favored : 92.94 % 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: 1.26 (0.17), residues: 2520 helix: 1.92 (0.13), residues: 1504 sheet: -0.75 (0.45), residues: 84 loop : -0.83 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 697 HIS 0.003 0.001 HIS A 289 PHE 0.012 0.001 PHE C 649 TYR 0.011 0.001 TYR B 653 ARG 0.002 0.000 ARG B 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 137 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 2.502 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 123 average time/residue: 1.1985 time to fit residues: 172.1272 Evaluate side-chains 118 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 2.326 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 1.2364 time to fit residues: 14.2830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 153 optimal weight: 0.0060 chunk 230 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 748 ASN C 378 HIS C 748 ASN D 378 HIS D 748 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21387 Z= 0.124 Angle : 0.420 5.472 28842 Z= 0.222 Chirality : 0.035 0.130 3223 Planarity : 0.003 0.029 3516 Dihedral : 17.898 176.329 3932 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.74 % Allowed : 7.01 % Favored : 91.25 % 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: 2.19 (0.13), residues: 1468 sheet: -0.70 (0.47), residues: 84 loop : -0.63 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 697 HIS 0.001 0.000 HIS B 289 PHE 0.008 0.001 PHE A 659 TYR 0.006 0.001 TYR B 194 ARG 0.002 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 139 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 2.504 Fit side-chains outliers start: 35 outliers final: 4 residues processed: 128 average time/residue: 1.1590 time to fit residues: 174.0833 Evaluate side-chains 105 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 3 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 207 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN C 378 HIS D 260 GLN D 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21387 Z= 0.261 Angle : 0.473 5.878 28842 Z= 0.246 Chirality : 0.038 0.184 3223 Planarity : 0.003 0.030 3516 Dihedral : 17.602 171.027 3932 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.89 % Allowed : 8.00 % Favored : 91.10 % 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: 1.38 (0.17), residues: 2520 helix: 1.97 (0.13), residues: 1496 sheet: -0.69 (0.47), residues: 84 loop : -0.65 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 697 HIS 0.002 0.001 HIS C 289 PHE 0.010 0.001 PHE C 649 TYR 0.009 0.001 TYR D 194 ARG 0.002 0.000 ARG C 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 118 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 2.294 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 113 average time/residue: 1.1980 time to fit residues: 157.6584 Evaluate side-chains 108 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.1594 time to fit residues: 7.0954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 378 HIS A 676 ASN B 260 GLN B 378 HIS B 676 ASN C 260 GLN C 378 HIS D 260 GLN D 378 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21387 Z= 0.148 Angle : 0.414 5.761 28842 Z= 0.219 Chirality : 0.035 0.136 3223 Planarity : 0.003 0.029 3516 Dihedral : 16.672 165.599 3932 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.04 % Allowed : 8.40 % Favored : 90.56 % 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: 1.49 (0.17), residues: 2520 helix: 2.06 (0.13), residues: 1488 sheet: -0.66 (0.49), residues: 84 loop : -0.58 (0.21), residues: 948 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 0.008 0.001 PHE C 649 TYR 0.007 0.001 TYR B 194 ARG 0.001 0.000 ARG D 212 *********************** 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 121 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 2.539 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 112 average time/residue: 1.2679 time to fit residues: 165.3723 Evaluate side-chains 108 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 1.2108 time to fit residues: 8.6102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 178 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 242 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN C 260 GLN C 378 HIS D 260 GLN D 378 HIS ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21387 Z= 0.298 Angle : 0.483 5.881 28842 Z= 0.251 Chirality : 0.038 0.184 3223 Planarity : 0.003 0.030 3516 Dihedral : 16.560 160.548 3932 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.24 % Allowed : 8.15 % Favored : 90.61 % 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: 1.42 (0.17), residues: 2520 helix: 1.97 (0.13), residues: 1476 sheet: -0.71 (0.49), residues: 84 loop : -0.53 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 697 HIS 0.002 0.001 HIS A 289 PHE 0.012 0.001 PHE A 304 TYR 0.010 0.001 TYR A 555 ARG 0.003 0.000 ARG B 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 125 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 2.364 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 116 average time/residue: 1.3071 time to fit residues: 175.8210 Evaluate side-chains 109 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 2.603 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 1.1976 time to fit residues: 9.8880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 190 optimal weight: 50.0000 chunk 220 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 378 HIS B 260 GLN B 378 HIS C 260 GLN C 378 HIS D 260 GLN D 378 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21387 Z= 0.189 Angle : 0.438 6.184 28842 Z= 0.229 Chirality : 0.036 0.145 3223 Planarity : 0.003 0.029 3516 Dihedral : 15.743 155.756 3932 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 8.25 % Favored : 90.51 % 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: 1.48 (0.17), residues: 2520 helix: 2.03 (0.13), residues: 1472 sheet: -0.62 (0.50), residues: 84 loop : -0.51 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.001 0.000 HIS A 289 PHE 0.009 0.001 PHE B 649 TYR 0.008 0.001 TYR B 194 ARG 0.001 0.000 ARG B 212 *********************** 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 125 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 2.382 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 116 average time/residue: 1.2022 time to fit residues: 163.3281 Evaluate side-chains 113 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 2.354 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 1.2096 time to fit residues: 10.0635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.6980 chunk 212 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 214 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 378 HIS B 260 GLN B 378 HIS C 260 GLN C 378 HIS ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 378 HIS D 676 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2030 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= 0.130 Angle : 0.408 7.066 28842 Z= 0.213 Chirality : 0.035 0.126 3223 Planarity : 0.003 0.029 3516 Dihedral : 14.412 149.308 3932 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.19 % Allowed : 8.50 % 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: 1.57 (0.17), residues: 2520 helix: 2.11 (0.14), residues: 1468 sheet: -0.59 (0.51), residues: 84 loop : -0.47 (0.21), residues: 968 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 0.008 0.001 PHE D 659 TYR 0.007 0.001 TYR A 555 ARG 0.001 0.000 ARG B 428 *********************** 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 127 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 2.638 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 119 average time/residue: 1.2075 time to fit residues: 167.8468 Evaluate side-chains 108 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 2.223 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.9405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 113 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 251 optimal weight: 0.0870 chunk 231 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 378 HIS B 260 GLN B 378 HIS C 260 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2050 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= 0.155 Angle : 0.421 7.128 28842 Z= 0.218 Chirality : 0.035 0.130 3223 Planarity : 0.003 0.029 3516 Dihedral : 14.081 146.843 3932 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.99 % Allowed : 8.90 % Favored : 90.11 % 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: 1.58 (0.17), residues: 2520 helix: 2.11 (0.14), residues: 1468 sheet: -0.50 (0.52), residues: 84 loop : -0.46 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 697 HIS 0.002 0.000 HIS C 378 PHE 0.007 0.001 PHE D 659 TYR 0.007 0.001 TYR D 555 ARG 0.001 0.000 ARG A 474 ********************** 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 121 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 2.437 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 117 average time/residue: 1.1713 time to fit residues: 160.7212 Evaluate side-chains 115 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 1.1580 time to fit residues: 8.4297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 0.0060 chunk 200 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 205 optimal weight: 0.0170 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 overall best weight: 1.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 378 HIS B 260 GLN B 378 HIS C 260 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.066196 restraints weight = 39144.884| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.52 r_work: 0.2759 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21387 Z= 0.169 Angle : 0.429 6.822 28842 Z= 0.223 Chirality : 0.036 0.136 3223 Planarity : 0.003 0.029 3516 Dihedral : 13.969 144.230 3932 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.04 % Allowed : 9.05 % Favored : 89.91 % 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: 1.54 (0.17), residues: 2520 helix: 2.07 (0.14), residues: 1468 sheet: -0.72 (0.43), residues: 116 loop : -0.43 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.002 0.000 HIS D 289 PHE 0.008 0.001 PHE B 649 TYR 0.007 0.001 TYR D 555 ARG 0.001 0.000 ARG C 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4876.26 seconds wall clock time: 89 minutes 0.77 seconds (5340.77 seconds total)