Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 03:03:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/07_2023/8sly_40583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/07_2023/8sly_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_40583/07_2023/8sly_40583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/07_2023/8sly_40583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/07_2023/8sly_40583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/07_2023/8sly_40583_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 9.02, per 1000 atoms: 0.49 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: 7.45 Conformation dependent library (CDL) restraints added in 2.9 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: 2.01 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: 5.37 Time building geometry restraints manager: 8.05 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: 10324 27.39 - 54.78: 368 54.78 - 82.17: 40 82.17 - 109.55: 4 109.55 - 136.94: 8 Dihedral angle restraints: 10744 sinusoidal: 3828 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 10741 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: 1.220 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: 0.020 Extract box with map and model: 7.670 Check model and map are aligned: 0.300 Set scattering table: 0.150 Process input model: 47.200 Find NCS groups from input model: 1.560 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.230 ------------------------------------------------------------------------------- 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 : 14.780 136.942 6264 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 % 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 *********************** 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 : 2.167 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2500 time to fit residues: 94.0074 Evaluate side-chains 166 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6835 ------------------------------------------------------------------------------- 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: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 18704 Z= 0.136 Angle : 0.469 7.927 25504 Z= 0.223 Chirality : 0.035 0.205 2976 Planarity : 0.003 0.036 3100 Dihedral : 7.846 87.627 2648 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.98 % 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: 1.94 (0.17), residues: 2316 helix: 2.37 (0.14), residues: 1384 sheet: 0.70 (0.51), residues: 112 loop : -0.55 (0.21), residues: 820 *********************** 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 : 2.109 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 193 average time/residue: 0.2308 time to fit residues: 76.5331 Evaluate side-chains 171 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1594 time to fit residues: 5.5514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8569 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 18704 Z= 0.168 Angle : 0.467 7.507 25504 Z= 0.221 Chirality : 0.036 0.196 2976 Planarity : 0.003 0.033 3100 Dihedral : 6.624 72.342 2648 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.98 % 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: 2.17 (0.18), residues: 2316 helix: 2.61 (0.14), residues: 1388 sheet: 0.66 (0.53), residues: 112 loop : -0.55 (0.21), residues: 816 *********************** 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 193 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 2.144 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 185 average time/residue: 0.2274 time to fit residues: 72.7259 Evaluate side-chains 171 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 2.118 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1579 time to fit residues: 5.5303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8548 moved from start: 0.2014 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= 0.132 Angle : 0.441 7.115 25504 Z= 0.209 Chirality : 0.035 0.128 2976 Planarity : 0.003 0.033 3100 Dihedral : 6.430 69.125 2648 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.81 % 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: 2.28 (0.18), residues: 2316 helix: 2.65 (0.14), residues: 1392 sheet: 0.76 (0.54), residues: 112 loop : -0.44 (0.22), residues: 812 *********************** 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 189 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 2.184 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 185 average time/residue: 0.2535 time to fit residues: 79.3426 Evaluate side-chains 169 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 2.222 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1643 time to fit residues: 5.4283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8555 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 18704 Z= 0.138 Angle : 0.449 7.673 25504 Z= 0.211 Chirality : 0.035 0.114 2976 Planarity : 0.003 0.033 3100 Dihedral : 6.296 68.563 2648 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.18), residues: 2316 helix: 2.71 (0.14), residues: 1388 sheet: 0.81 (0.55), residues: 112 loop : -0.42 (0.22), residues: 816 *********************** 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 184 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 2.151 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 183 average time/residue: 0.2579 time to fit residues: 77.8809 Evaluate side-chains 167 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 2.394 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2101 time to fit residues: 3.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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: 0.8625 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 18704 Z= 0.273 Angle : 0.513 7.691 25504 Z= 0.244 Chirality : 0.037 0.178 2976 Planarity : 0.003 0.033 3100 Dihedral : 6.662 69.407 2648 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.87 % 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: 2.23 (0.18), residues: 2316 helix: 2.61 (0.14), residues: 1380 sheet: 0.63 (0.53), residues: 112 loop : -0.40 (0.22), residues: 824 *********************** 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 182 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 2.142 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 179 average time/residue: 0.2602 time to fit residues: 77.3269 Evaluate side-chains 162 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1734 time to fit residues: 5.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8571 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 18704 Z= 0.136 Angle : 0.469 7.900 25504 Z= 0.218 Chirality : 0.035 0.114 2976 Planarity : 0.003 0.033 3100 Dihedral : 6.411 70.010 2648 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.35 % 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: 2.33 (0.18), residues: 2316 helix: 2.67 (0.14), residues: 1392 sheet: 0.66 (0.53), residues: 112 loop : -0.37 (0.22), residues: 812 *********************** 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 189 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 2.307 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 186 average time/residue: 0.2644 time to fit residues: 81.2827 Evaluate side-chains 171 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 2.066 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1569 time to fit residues: 3.5742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 135 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 0.0070 chunk 178 optimal weight: 0.2980 chunk 206 optimal weight: 0.8980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 18704 Z= 0.116 Angle : 0.456 10.422 25504 Z= 0.212 Chirality : 0.034 0.111 2976 Planarity : 0.003 0.032 3100 Dihedral : 5.959 68.123 2648 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.06 % 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: 2.79 (0.14), residues: 1376 sheet: 0.73 (0.53), residues: 112 loop : -0.42 (0.21), residues: 828 *********************** 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 185 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.102 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.2556 time to fit residues: 78.1304 Evaluate side-chains 170 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 2.274 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1661 time to fit residues: 3.2536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.2980 chunk 198 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 166 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 191 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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: 0.8532 moved from start: 0.2529 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= 0.118 Angle : 0.454 7.110 25504 Z= 0.208 Chirality : 0.035 0.114 2976 Planarity : 0.003 0.032 3100 Dihedral : 5.851 66.884 2648 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 2316 helix: 2.81 (0.14), residues: 1376 sheet: 0.76 (0.53), residues: 112 loop : -0.43 (0.21), residues: 828 *********************** 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 177 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 175 average time/residue: 0.2527 time to fit residues: 74.4904 Evaluate side-chains 165 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 2.143 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1595 time to fit residues: 3.1292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 235 optimal weight: 10.0000 chunk 216 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8541 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 18704 Z= 0.140 Angle : 0.483 10.275 25504 Z= 0.220 Chirality : 0.035 0.111 2976 Planarity : 0.003 0.032 3100 Dihedral : 5.753 65.028 2648 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 0.00 % 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: 2.41 (0.18), residues: 2316 helix: 2.82 (0.14), residues: 1376 sheet: 0.75 (0.53), residues: 112 loop : -0.43 (0.21), residues: 828 ********************** 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 171 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2446 time to fit residues: 72.2269 Evaluate side-chains 161 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 5.9990 chunk 172 optimal weight: 0.0020 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080859 restraints weight = 38866.285| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.22 r_work: 0.2973 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 18704 Z= 0.146 Angle : 0.483 9.819 25504 Z= 0.221 Chirality : 0.035 0.156 2976 Planarity : 0.003 0.032 3100 Dihedral : 5.710 64.252 2648 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.00 % 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: 2.41 (0.18), residues: 2316 helix: 2.78 (0.14), residues: 1380 sheet: 0.75 (0.53), residues: 112 loop : -0.40 (0.22), residues: 824 =============================================================================== Job complete usr+sys time: 3180.80 seconds wall clock time: 59 minutes 6.79 seconds (3546.79 seconds total)