Starting phenix.real_space_refine on Sun Mar 17 15:58:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/03_2024/8sly_40583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/03_2024/8sly_40583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/03_2024/8sly_40583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/03_2024/8sly_40583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/03_2024/8sly_40583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/03_2024/8sly_40583_updated.pdb" } resolution = 3.32 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 Na 1 4.78 5 C 12092 2.51 5 N 3028 2.21 5 O 3044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18257 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 227 Chain: "B" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 227 Chain: "C" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 227 Chain: "D" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 227 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {' NA': 1, 'P0T': 2, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'P0T': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'P0T': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'P0T': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.74, per 1000 atoms: 0.53 Number of scatterers: 18257 At special positions: 0 Unit cell: (156.04, 156.04, 112.05, 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 88 16.00 P 4 15.00 Na 1 11.00 O 3044 8.00 N 3028 7.00 C 12092 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: 6.97 Conformation dependent library (CDL) restraints added in 3.2 seconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 58.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.666A pdb=" N LYS A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.657A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 367 through 373 removed outlier: 4.634A pdb=" N HIS A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 removed outlier: 3.506A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 412 Processing helix chain 'A' and resid 434 through 458 Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 471 through 491 Processing helix chain 'A' and resid 497 through 518 removed outlier: 3.960A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 559 Processing helix chain 'A' and resid 592 through 604 removed outlier: 3.671A pdb=" N ALA A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 649 removed outlier: 3.690A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.665A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 135 through 145 removed outlier: 3.666A pdb=" N LYS B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.657A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 281 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 367 through 373 removed outlier: 4.634A pdb=" N HIS B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 388 removed outlier: 3.505A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 412 Processing helix chain 'B' and resid 434 through 458 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 471 through 491 Processing helix chain 'B' and resid 497 through 518 removed outlier: 3.960A pdb=" N LEU B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 559 Processing helix chain 'B' and resid 592 through 604 removed outlier: 3.671A pdb=" N ALA B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 649 removed outlier: 3.690A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 673 removed outlier: 3.665A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 135 through 145 removed outlier: 3.666A pdb=" N LYS C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.657A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 213 through 220 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 367 through 373 removed outlier: 4.634A pdb=" N HIS C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 371 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 388 removed outlier: 3.506A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 412 Processing helix chain 'C' and resid 434 through 458 Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 471 through 491 Processing helix chain 'C' and resid 497 through 518 removed outlier: 3.960A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 559 Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.671A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 649 removed outlier: 3.690A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 673 removed outlier: 3.664A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 135 through 145 removed outlier: 3.666A pdb=" N LYS D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.657A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 281 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 367 through 373 removed outlier: 4.635A pdb=" N HIS D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG D 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 388 removed outlier: 3.506A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 383 " --> pdb=" O ASN D 379 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 412 Processing helix chain 'D' and resid 434 through 458 Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 471 through 491 Processing helix chain 'D' and resid 497 through 518 removed outlier: 3.960A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLY D 518 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 559 Processing helix chain 'D' and resid 592 through 604 removed outlier: 3.671A pdb=" N ALA D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 649 removed outlier: 3.690A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 673 removed outlier: 3.665A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 329 through 331 Processing sheet with id= B, first strand: chain 'B' and resid 329 through 331 Processing sheet with id= C, first strand: chain 'C' and resid 329 through 331 Processing sheet with id= D, first strand: chain 'D' and resid 329 through 331 896 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2949 1.32 - 1.45: 5167 1.45 - 1.57: 10428 1.57 - 1.69: 32 1.69 - 1.82: 128 Bond restraints: 18704 Sorted by residual: bond pdb=" C05 P0T C 801 " pdb=" C06 P0T C 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C05 P0T D 801 " pdb=" C06 P0T D 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C05 P0T A 801 " pdb=" C06 P0T A 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" C05 P0T B 801 " pdb=" C06 P0T B 801 " ideal model delta sigma weight residual 1.521 1.656 -0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C03 P0T C 801 " pdb=" C04 P0T C 801 " ideal model delta sigma weight residual 1.548 1.679 -0.131 2.00e-02 2.50e+03 4.30e+01 ... (remaining 18699 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.24: 548 107.24 - 113.94: 10736 113.94 - 120.64: 7953 120.64 - 127.34: 6016 127.34 - 134.04: 251 Bond angle restraints: 25504 Sorted by residual: angle pdb=" N ILE A 605 " pdb=" CA ILE A 605 " pdb=" C ILE A 605 " ideal model delta sigma weight residual 112.98 108.73 4.25 1.25e+00 6.40e-01 1.15e+01 angle pdb=" N ILE D 605 " pdb=" CA ILE D 605 " pdb=" C ILE D 605 " ideal model delta sigma weight residual 112.98 108.74 4.24 1.25e+00 6.40e-01 1.15e+01 angle pdb=" N ILE B 605 " pdb=" CA ILE B 605 " pdb=" C ILE B 605 " ideal model delta sigma weight residual 112.98 108.76 4.22 1.25e+00 6.40e-01 1.14e+01 angle pdb=" N ILE C 605 " pdb=" CA ILE C 605 " pdb=" C ILE C 605 " ideal model delta sigma weight residual 112.98 108.76 4.22 1.25e+00 6.40e-01 1.14e+01 angle pdb=" C22 POV D 803 " pdb=" C21 POV D 803 " pdb=" O21 POV D 803 " ideal model delta sigma weight residual 111.03 120.99 -9.96 3.00e+00 1.11e-01 1.10e+01 ... (remaining 25499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 10448 27.39 - 54.78: 396 54.78 - 82.17: 40 82.17 - 109.55: 4 109.55 - 136.94: 8 Dihedral angle restraints: 10896 sinusoidal: 3980 harmonic: 6916 Sorted by residual: dihedral pdb=" C18 P0T B 801 " pdb=" C20 P0T B 801 " pdb=" C21 P0T B 801 " pdb=" C22 P0T B 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.35 136.94 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C18 P0T C 801 " pdb=" C20 P0T C 801 " pdb=" C21 P0T C 801 " pdb=" C22 P0T C 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.36 136.93 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C18 P0T A 801 " pdb=" C20 P0T A 801 " pdb=" C21 P0T A 801 " pdb=" C22 P0T A 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.36 136.93 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 10893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2949 0.112 - 0.223: 19 0.223 - 0.335: 0 0.335 - 0.447: 0 0.447 - 0.559: 8 Chirality restraints: 2976 Sorted by residual: chirality pdb=" C03 P0T C 802 " pdb=" C04 P0T C 802 " pdb=" C05 P0T C 802 " pdb=" C10 P0T C 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C03 P0T A 802 " pdb=" C04 P0T A 802 " pdb=" C05 P0T A 802 " pdb=" C10 P0T A 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C03 P0T B 802 " pdb=" C04 P0T B 802 " pdb=" C05 P0T B 802 " pdb=" C10 P0T B 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 ... (remaining 2973 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 604 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C THR C 604 " 0.029 2.00e-02 2.50e+03 pdb=" O THR C 604 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 605 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 604 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR A 604 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 604 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 605 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 604 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C THR B 604 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 604 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 605 " 0.010 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1783 2.74 - 3.28: 18201 3.28 - 3.82: 30447 3.82 - 4.36: 35561 4.36 - 4.90: 60822 Nonbonded interactions: 146814 Sorted by model distance: nonbonded pdb=" OH TYR C 544 " pdb=" OG1 THR C 604 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR A 544 " pdb=" OG1 THR A 604 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR D 544 " pdb=" OG1 THR D 604 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR B 544 " pdb=" OG1 THR B 604 " model vdw 2.206 2.440 nonbonded pdb=" O ALA D 361 " pdb=" NH1 ARG D 369 " model vdw 2.302 2.520 ... (remaining 146809 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 75 through 728 or resid 801 through 802)) selection = (chain 'B' and (resid 75 through 728 or resid 801 through 802)) selection = (chain 'C' and (resid 75 through 728 or resid 801 through 802)) selection = (chain 'D' and (resid 75 through 728 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.980 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 47.590 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.006 0.136 18704 Z= 0.414 Angle : 0.665 9.959 25504 Z= 0.297 Chirality : 0.046 0.559 2976 Planarity : 0.003 0.047 3100 Dihedral : 15.008 136.942 6416 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2316 helix: 1.76 (0.14), residues: 1376 sheet: 0.44 (0.50), residues: 112 loop : -0.50 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 454 HIS 0.001 0.000 HIS D 413 PHE 0.023 0.001 PHE C 362 TYR 0.016 0.001 TYR B 162 ARG 0.006 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.007 Fit side-chains REVERT: A 349 ASP cc_start: 0.8840 (t70) cc_final: 0.8586 (t0) REVERT: B 349 ASP cc_start: 0.8910 (t70) cc_final: 0.8687 (t0) REVERT: C 349 ASP cc_start: 0.8862 (t70) cc_final: 0.8649 (t0) REVERT: D 349 ASP cc_start: 0.8880 (t70) cc_final: 0.8628 (t0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2312 time to fit residues: 86.0610 Evaluate side-chains 166 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 3.9990 chunk 178 optimal weight: 0.0060 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 184 optimal weight: 0.0270 chunk 71 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 overall best weight: 0.7856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 127 ASN C 127 ASN D 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18704 Z= 0.137 Angle : 0.468 7.586 25504 Z= 0.223 Chirality : 0.035 0.184 2976 Planarity : 0.003 0.036 3100 Dihedral : 8.513 88.136 2800 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.98 % Allowed : 6.08 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.18), residues: 2316 helix: 2.39 (0.14), residues: 1384 sheet: 0.70 (0.51), residues: 112 loop : -0.55 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 454 HIS 0.003 0.000 HIS A 413 PHE 0.015 0.001 PHE C 407 TYR 0.014 0.001 TYR A 471 ARG 0.001 0.000 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 2.066 Fit side-chains REVERT: A 349 ASP cc_start: 0.8809 (t70) cc_final: 0.8540 (t0) REVERT: A 645 MET cc_start: 0.8456 (mmm) cc_final: 0.8250 (mmt) REVERT: B 349 ASP cc_start: 0.8882 (t70) cc_final: 0.8637 (t0) REVERT: B 645 MET cc_start: 0.8393 (mmm) cc_final: 0.8118 (mmt) REVERT: C 349 ASP cc_start: 0.8811 (t70) cc_final: 0.8601 (t0) REVERT: C 645 MET cc_start: 0.8455 (mmm) cc_final: 0.7897 (mmt) REVERT: D 349 ASP cc_start: 0.8870 (t70) cc_final: 0.8608 (t0) REVERT: D 638 LEU cc_start: 0.9235 (tt) cc_final: 0.8932 (tt) outliers start: 17 outliers final: 9 residues processed: 193 average time/residue: 0.2291 time to fit residues: 75.1147 Evaluate side-chains 172 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 178 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18704 Z= 0.178 Angle : 0.466 7.269 25504 Z= 0.223 Chirality : 0.036 0.158 2976 Planarity : 0.003 0.032 3100 Dihedral : 7.423 72.456 2800 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.74 % Allowed : 7.87 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2316 helix: 2.64 (0.14), residues: 1388 sheet: 0.67 (0.53), residues: 112 loop : -0.53 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 454 HIS 0.003 0.001 HIS B 313 PHE 0.012 0.001 PHE C 407 TYR 0.014 0.001 TYR A 471 ARG 0.002 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 2.020 Fit side-chains REVERT: A 349 ASP cc_start: 0.8799 (t70) cc_final: 0.8527 (t0) REVERT: B 349 ASP cc_start: 0.8828 (t70) cc_final: 0.8582 (t0) REVERT: B 638 LEU cc_start: 0.9373 (tt) cc_final: 0.9143 (tt) REVERT: C 349 ASP cc_start: 0.8813 (t70) cc_final: 0.8550 (t0) REVERT: C 645 MET cc_start: 0.8092 (mmm) cc_final: 0.7884 (mmt) REVERT: D 349 ASP cc_start: 0.8828 (t70) cc_final: 0.8575 (t0) outliers start: 30 outliers final: 21 residues processed: 195 average time/residue: 0.2242 time to fit residues: 74.0832 Evaluate side-chains 180 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 632 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18704 Z= 0.134 Angle : 0.445 7.692 25504 Z= 0.211 Chirality : 0.035 0.125 2976 Planarity : 0.003 0.033 3100 Dihedral : 7.163 72.675 2800 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.56 % Allowed : 9.78 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.18), residues: 2316 helix: 2.70 (0.14), residues: 1380 sheet: 0.75 (0.54), residues: 112 loop : -0.45 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 454 HIS 0.002 0.000 HIS B 413 PHE 0.015 0.001 PHE B 407 TYR 0.010 0.001 TYR A 471 ARG 0.001 0.000 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 2.392 Fit side-chains REVERT: A 349 ASP cc_start: 0.8803 (t70) cc_final: 0.8528 (t0) REVERT: A 645 MET cc_start: 0.7882 (mmt) cc_final: 0.7679 (tpt) REVERT: B 349 ASP cc_start: 0.8818 (t70) cc_final: 0.8564 (t0) REVERT: C 349 ASP cc_start: 0.8805 (t70) cc_final: 0.8553 (t0) REVERT: D 349 ASP cc_start: 0.8823 (t70) cc_final: 0.8568 (t0) REVERT: D 638 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9057 (tt) outliers start: 27 outliers final: 19 residues processed: 191 average time/residue: 0.2258 time to fit residues: 73.6074 Evaluate side-chains 179 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 638 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18704 Z= 0.335 Angle : 0.550 7.519 25504 Z= 0.263 Chirality : 0.038 0.156 2976 Planarity : 0.003 0.034 3100 Dihedral : 7.799 75.263 2800 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.26 % Allowed : 11.00 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.18), residues: 2316 helix: 2.46 (0.14), residues: 1380 sheet: 0.44 (0.52), residues: 112 loop : -0.45 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 454 HIS 0.004 0.001 HIS A 251 PHE 0.017 0.002 PHE A 407 TYR 0.016 0.001 TYR A 471 ARG 0.002 0.000 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 2.270 Fit side-chains REVERT: A 349 ASP cc_start: 0.8823 (t70) cc_final: 0.8567 (t0) REVERT: A 638 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9200 (tt) REVERT: A 645 MET cc_start: 0.8244 (mmt) cc_final: 0.7927 (tpt) REVERT: B 349 ASP cc_start: 0.8831 (t70) cc_final: 0.8582 (t0) REVERT: C 349 ASP cc_start: 0.8827 (t70) cc_final: 0.8576 (t0) REVERT: D 349 ASP cc_start: 0.8819 (t70) cc_final: 0.8567 (t0) REVERT: D 638 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9179 (tp) outliers start: 39 outliers final: 27 residues processed: 182 average time/residue: 0.2422 time to fit residues: 73.4473 Evaluate side-chains 170 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 683 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.7980 chunk 205 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18704 Z= 0.170 Angle : 0.468 7.395 25504 Z= 0.221 Chirality : 0.035 0.123 2976 Planarity : 0.003 0.033 3100 Dihedral : 7.338 70.386 2800 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.79 % Allowed : 11.92 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.18), residues: 2316 helix: 2.56 (0.14), residues: 1392 sheet: 0.52 (0.52), residues: 112 loop : -0.38 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 454 HIS 0.002 0.000 HIS B 313 PHE 0.014 0.001 PHE B 407 TYR 0.010 0.001 TYR A 471 ARG 0.002 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 2.364 Fit side-chains REVERT: A 349 ASP cc_start: 0.8808 (t70) cc_final: 0.8555 (t0) REVERT: A 638 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9149 (tt) REVERT: B 349 ASP cc_start: 0.8816 (t70) cc_final: 0.8549 (t0) REVERT: C 349 ASP cc_start: 0.8796 (t70) cc_final: 0.8545 (t0) REVERT: C 645 MET cc_start: 0.8168 (mmt) cc_final: 0.7952 (tpt) REVERT: D 349 ASP cc_start: 0.8815 (t70) cc_final: 0.8552 (t0) REVERT: D 638 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9168 (tp) outliers start: 31 outliers final: 22 residues processed: 187 average time/residue: 0.2499 time to fit residues: 76.6508 Evaluate side-chains 178 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 638 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 0.0060 chunk 105 optimal weight: 10.0000 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18704 Z= 0.202 Angle : 0.499 8.882 25504 Z= 0.231 Chirality : 0.035 0.126 2976 Planarity : 0.003 0.034 3100 Dihedral : 7.260 70.607 2800 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.85 % Allowed : 12.50 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.18), residues: 2316 helix: 2.61 (0.14), residues: 1384 sheet: 0.56 (0.52), residues: 112 loop : -0.44 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 454 HIS 0.002 0.001 HIS D 313 PHE 0.014 0.001 PHE B 407 TYR 0.011 0.001 TYR A 471 ARG 0.003 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 2.246 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8805 (t70) cc_final: 0.8530 (t0) REVERT: A 638 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9181 (tt) REVERT: B 349 ASP cc_start: 0.8806 (t70) cc_final: 0.8539 (t0) REVERT: C 349 ASP cc_start: 0.8804 (t70) cc_final: 0.8533 (t0) REVERT: D 349 ASP cc_start: 0.8809 (t70) cc_final: 0.8538 (t0) REVERT: D 638 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9192 (tp) outliers start: 32 outliers final: 26 residues processed: 184 average time/residue: 0.2493 time to fit residues: 75.6370 Evaluate side-chains 185 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 683 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 112 optimal weight: 0.4980 chunk 21 optimal weight: 0.0770 chunk 178 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 438 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18704 Z= 0.133 Angle : 0.468 10.212 25504 Z= 0.214 Chirality : 0.034 0.113 2976 Planarity : 0.003 0.033 3100 Dihedral : 6.866 69.463 2800 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.56 % Allowed : 12.96 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.18), residues: 2316 helix: 2.73 (0.14), residues: 1380 sheet: 0.68 (0.53), residues: 112 loop : -0.41 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 454 HIS 0.002 0.000 HIS D 413 PHE 0.012 0.001 PHE B 407 TYR 0.007 0.001 TYR A 471 ARG 0.003 0.000 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 2.178 Fit side-chains REVERT: A 144 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8832 (pttp) REVERT: A 349 ASP cc_start: 0.8815 (t70) cc_final: 0.8545 (t0) REVERT: B 349 ASP cc_start: 0.8818 (t70) cc_final: 0.8555 (t0) REVERT: C 349 ASP cc_start: 0.8813 (t70) cc_final: 0.8545 (t0) REVERT: D 349 ASP cc_start: 0.8818 (t70) cc_final: 0.8550 (t0) outliers start: 27 outliers final: 25 residues processed: 199 average time/residue: 0.2369 time to fit residues: 78.5961 Evaluate side-chains 192 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 0.4980 chunk 200 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18704 Z= 0.182 Angle : 0.478 8.704 25504 Z= 0.221 Chirality : 0.035 0.120 2976 Planarity : 0.003 0.034 3100 Dihedral : 6.926 69.076 2800 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.85 % Allowed : 12.91 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.18), residues: 2316 helix: 2.75 (0.14), residues: 1384 sheet: 0.60 (0.52), residues: 112 loop : -0.44 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 454 HIS 0.002 0.000 HIS D 165 PHE 0.013 0.001 PHE B 407 TYR 0.010 0.001 TYR A 471 ARG 0.003 0.000 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 2.095 Fit side-chains REVERT: A 349 ASP cc_start: 0.8830 (t70) cc_final: 0.8567 (t0) REVERT: B 349 ASP cc_start: 0.8832 (t70) cc_final: 0.8572 (t0) REVERT: C 349 ASP cc_start: 0.8827 (t70) cc_final: 0.8564 (t0) REVERT: D 349 ASP cc_start: 0.8830 (t70) cc_final: 0.8566 (t0) outliers start: 32 outliers final: 25 residues processed: 191 average time/residue: 0.2356 time to fit residues: 74.7749 Evaluate side-chains 189 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 235 optimal weight: 0.0670 chunk 216 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18704 Z= 0.145 Angle : 0.469 8.451 25504 Z= 0.216 Chirality : 0.035 0.111 2976 Planarity : 0.003 0.034 3100 Dihedral : 6.749 67.402 2800 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.45 % Allowed : 13.37 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.18), residues: 2316 helix: 2.81 (0.14), residues: 1376 sheet: 0.62 (0.52), residues: 112 loop : -0.44 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 454 HIS 0.002 0.000 HIS B 165 PHE 0.012 0.001 PHE B 407 TYR 0.008 0.001 TYR A 471 ARG 0.003 0.000 ARG B 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.967 Fit side-chains REVERT: A 349 ASP cc_start: 0.8819 (t70) cc_final: 0.8561 (t0) REVERT: B 349 ASP cc_start: 0.8825 (t70) cc_final: 0.8571 (t0) REVERT: C 349 ASP cc_start: 0.8809 (t70) cc_final: 0.8549 (t0) REVERT: D 349 ASP cc_start: 0.8825 (t70) cc_final: 0.8567 (t0) outliers start: 25 outliers final: 24 residues processed: 189 average time/residue: 0.2469 time to fit residues: 76.7190 Evaluate side-chains 191 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.079683 restraints weight = 38776.787| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.26 r_work: 0.2955 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18704 Z= 0.138 Angle : 0.476 10.149 25504 Z= 0.217 Chirality : 0.034 0.125 2976 Planarity : 0.003 0.034 3100 Dihedral : 6.555 66.235 2800 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.56 % Allowed : 13.37 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.18), residues: 2316 helix: 2.83 (0.14), residues: 1380 sheet: 0.64 (0.52), residues: 112 loop : -0.40 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 454 HIS 0.002 0.000 HIS A 165 PHE 0.012 0.001 PHE B 407 TYR 0.008 0.001 TYR A 471 ARG 0.003 0.000 ARG B 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3283.47 seconds wall clock time: 60 minutes 18.72 seconds (3618.72 seconds total)