Starting phenix.real_space_refine on Thu Mar 5 10:14:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7px8_13691/03_2026/7px8_13691.cif Found real_map, /net/cci-nas-00/data/ceres_data/7px8_13691/03_2026/7px8_13691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7px8_13691/03_2026/7px8_13691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7px8_13691/03_2026/7px8_13691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7px8_13691/03_2026/7px8_13691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7px8_13691/03_2026/7px8_13691.map" } resolution = 3.27 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 13755 2.51 5 N 3683 2.21 5 O 3827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21409 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5338 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 700, 5279 Classifications: {'peptide': 700} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 653} Chain breaks: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 7, 'TYR:plan': 1, 'ASP:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 159 Conformer: "B" Number of residues, atoms: 700, 5279 Classifications: {'peptide': 700} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 653} Chain breaks: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 7, 'TYR:plan': 1, 'ASP:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 159 bond proxies already assigned to first conformer: 5358 Chain: "B" Number of atoms: 5359 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 700, 5293 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 653} Chain breaks: 3 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 7, 'TYR:plan': 1, 'ASP:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 143 Conformer: "B" Number of residues, atoms: 700, 5293 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 653} Chain breaks: 3 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 7, 'TYR:plan': 1, 'ASP:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 143 bond proxies already assigned to first conformer: 5364 Chain: "C" Number of atoms: 5360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 699, 5294 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 7, 'ASP:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 133 Conformer: "B" Number of residues, atoms: 699, 5294 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 7, 'ASP:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 133 bond proxies already assigned to first conformer: 5364 Chain: "D" Number of atoms: 5352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 699, 5297 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 7, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 132 Conformer: "B" Number of residues, atoms: 699, 5297 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 7, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 132 bond proxies already assigned to first conformer: 5379 Residues with excluded nonbonded symmetry interactions: 30 residue: pdb=" N AMET A 584 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 584 " occ=0.50 residue: pdb=" N AGLY A 585 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 585 " occ=0.50 residue: pdb=" N AGLY A 586 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 586 " occ=0.50 residue: pdb=" N ASER A 587 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 587 " occ=0.50 residue: pdb=" N AHIS A 588 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 588 " occ=0.50 residue: pdb=" N AGLY A 589 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 589 " occ=0.50 residue: pdb=" N AGLY A 590 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 590 " occ=0.50 residue: pdb=" N APHE A 591 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 591 " occ=0.50 residue: pdb=" N AMET B 584 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 584 " occ=0.50 residue: pdb=" N AGLY B 585 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 585 " occ=0.50 residue: pdb=" N AGLY B 586 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 586 " occ=0.50 residue: pdb=" N ASER B 587 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 587 " occ=0.50 ... (remaining 18 not shown) Time building chain proxies: 8.81, per 1000 atoms: 0.41 Number of scatterers: 21409 At special positions: 0 Unit cell: (135.85, 90.25, 132.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 3827 8.00 N 3683 7.00 C 13755 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 - 3.00 Amino acid : True - 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: 1.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 42 sheets defined 19.4% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.900A pdb=" N GLU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.655A pdb=" N ILE A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 587 through 600 removed outlier: 5.204A pdb=" N BPHE A 591 " --> pdb=" O BSER A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 626 through 634 removed outlier: 3.757A pdb=" N MET A 630 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 655 Processing helix chain 'A' and resid 680 through 693 Processing helix chain 'A' and resid 711 through 731 removed outlier: 3.635A pdb=" N THR A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 729 " --> pdb=" O TRP A 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.965A pdb=" N GLU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.694A pdb=" N ILE B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 587 through 600 removed outlier: 4.988A pdb=" N BPHE B 591 " --> pdb=" O BSER B 587 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 595 " --> pdb=" O BPHE B 591 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 598 " --> pdb=" O CYS B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 622 removed outlier: 4.558A pdb=" N GLY B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 634 removed outlier: 3.864A pdb=" N MET B 630 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 655 Processing helix chain 'B' and resid 659 through 663 Processing helix chain 'B' and resid 680 through 693 removed outlier: 3.503A pdb=" N ARG B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 730 Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.921A pdb=" N GLU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.600A pdb=" N ILE C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 572 removed outlier: 3.621A pdb=" N GLN C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 626 through 634 removed outlier: 4.098A pdb=" N MET C 630 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 654 removed outlier: 3.687A pdb=" N LYS C 654 " --> pdb=" O ALA C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 removed outlier: 3.518A pdb=" N TYR C 659 " --> pdb=" O PRO C 656 " (cutoff:3.500A) Proline residue: C 661 - end of helix Processing helix chain 'C' and resid 680 through 693 removed outlier: 3.521A pdb=" N MET C 684 " --> pdb=" O PHE C 680 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 731 removed outlier: 3.534A pdb=" N SER C 716 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP C 717 " --> pdb=" O GLU C 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.906A pdb=" N GLU D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 139' Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 519 through 527 Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.630A pdb=" N ILE D 548 " --> pdb=" O GLY D 544 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 573 removed outlier: 4.300A pdb=" N GLU D 573 " --> pdb=" O GLN D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'D' and resid 615 through 622 removed outlier: 4.277A pdb=" N GLY D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 634 removed outlier: 3.838A pdb=" N MET D 630 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 655 Processing helix chain 'D' and resid 656 through 663 Proline residue: D 661 - end of helix Processing helix chain 'D' and resid 680 through 693 removed outlier: 3.570A pdb=" N ARG D 693 " --> pdb=" O VAL D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 31 removed outlier: 5.534A pdb=" N LEU A 26 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 51 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 28 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG A 42 " --> pdb=" O HIS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.146A pdb=" N ARG A 42 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG A 62 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 96 removed outlier: 5.718A pdb=" N GLU A 91 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS A 108 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 131 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU A 125 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 251 removed outlier: 6.584A pdb=" N TRP A 263 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN A 248 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL A 261 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.612A pdb=" N ALA A 301 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 315 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU A 307 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG A 313 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 331 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 340 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 382 removed outlier: 3.571A pdb=" N SER A 380 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 387 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 409 through 416 removed outlier: 5.521A pdb=" N TRP A 410 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER A 425 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 412 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN A 423 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 414 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 433 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 461 through 468 removed outlier: 3.729A pdb=" N GLU A 485 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 503 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 535 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N MET A 505 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 606 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 670 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 25 through 31 removed outlier: 5.516A pdb=" N LEU B 26 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 51 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 28 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 36 removed outlier: 4.477A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG B 62 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 96 removed outlier: 5.947A pdb=" N GLU B 91 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS B 108 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 93 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLN B 119 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN B 134 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 121 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 132 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 123 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB6, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 251 removed outlier: 6.457A pdb=" N TRP B 263 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLN B 248 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 261 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.595A pdb=" N ALA B 301 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 315 " --> pdb=" O PRO B 305 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU B 307 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG B 313 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 340 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 381 removed outlier: 3.615A pdb=" N SER B 380 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 387 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 409 through 416 removed outlier: 5.581A pdb=" N TRP B 410 " --> pdb=" O SER B 425 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER B 425 " --> pdb=" O TRP B 410 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU B 412 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN B 423 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 433 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 461 through 468 removed outlier: 3.719A pdb=" N GLU B 485 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N VAL B 500 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG B 580 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 502 " --> pdb=" O ARG B 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 585 through 586 Processing sheet with id=AC4, first strand: chain 'C' and resid 25 through 31 removed outlier: 6.600A pdb=" N GLU C 49 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA C 29 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS C 47 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU C 31 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR C 45 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 35 through 36 removed outlier: 4.274A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG C 62 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 96 removed outlier: 5.959A pdb=" N GLU C 91 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS C 108 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 93 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 131 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU C 125 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AC8, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AC9, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AD1, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AD2, first strand: chain 'C' and resid 301 through 307 removed outlier: 3.564A pdb=" N ALA C 301 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 315 " --> pdb=" O PRO C 305 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU C 307 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 313 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 375 through 382 removed outlier: 3.567A pdb=" N SER C 380 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 387 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 409 through 416 removed outlier: 5.632A pdb=" N TRP C 410 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER C 425 " --> pdb=" O TRP C 410 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU C 412 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN C 423 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 414 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 433 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 461 through 468 removed outlier: 3.589A pdb=" N GLU C 485 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 535 " --> pdb=" O MET C 505 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N VAL C 500 " --> pdb=" O ALA C 578 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG C 580 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 606 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 25 through 31 removed outlier: 6.735A pdb=" N GLU D 49 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 29 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS D 47 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU D 31 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 45 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 35 through 36 removed outlier: 4.242A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG D 62 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 91 through 96 removed outlier: 6.836A pdb=" N LEU D 106 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER D 94 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA D 104 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU D 96 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N MET D 102 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU D 125 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AE1, first strand: chain 'D' and resid 173 through 174 Processing sheet with id=AE2, first strand: chain 'D' and resid 244 through 251 removed outlier: 6.573A pdb=" N TRP D 263 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN D 248 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL D 261 " --> pdb=" O GLN D 248 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 301 through 307 removed outlier: 3.592A pdb=" N ALA D 301 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 315 " --> pdb=" O PRO D 305 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU D 307 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG D 313 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 331 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 375 through 382 Processing sheet with id=AE5, first strand: chain 'D' and resid 409 through 416 removed outlier: 5.470A pdb=" N TRP D 410 " --> pdb=" O SER D 425 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER D 425 " --> pdb=" O TRP D 410 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 412 " --> pdb=" O GLN D 423 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN D 423 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 433 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 461 through 468 removed outlier: 3.870A pdb=" N GLU D 485 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 535 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET D 502 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N AMET D 584 " --> pdb=" O MET D 502 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL D 504 " --> pdb=" O AMET D 584 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N AGLY D 586 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 610 " --> pdb=" O BGLY D 585 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N BSER D 587 " --> pdb=" O ARG D 610 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY D 672 " --> pdb=" O ASN D 611 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2382 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: 4.86 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6923 1.34 - 1.46: 4673 1.46 - 1.58: 10187 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 21999 Sorted by residual: bond pdb=" CG PRO B 552 " pdb=" CD PRO B 552 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.69e+00 bond pdb=" CB PRO D 459 " pdb=" CG PRO D 459 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.28e+00 bond pdb=" CB PRO C 459 " pdb=" CG PRO C 459 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.28e+00 bond pdb=" CB PRO B 552 " pdb=" CG PRO B 552 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.10e+00 bond pdb=" C ILE A 272 " pdb=" O ILE A 272 " ideal model delta sigma weight residual 1.236 1.225 0.012 1.19e-02 7.06e+03 9.51e-01 ... (remaining 21994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 29343 1.50 - 2.99: 537 2.99 - 4.49: 89 4.49 - 5.98: 20 5.98 - 7.48: 3 Bond angle restraints: 29992 Sorted by residual: angle pdb=" C LYS D 126 " pdb=" CA LYS D 126 " pdb=" CB LYS D 126 " ideal model delta sigma weight residual 117.23 110.33 6.90 1.36e+00 5.41e-01 2.58e+01 angle pdb=" CA PRO B 552 " pdb=" N PRO B 552 " pdb=" CD PRO B 552 " ideal model delta sigma weight residual 112.00 106.68 5.32 1.40e+00 5.10e-01 1.44e+01 angle pdb=" CA LYS D 126 " pdb=" C LYS D 126 " pdb=" N ASN D 127 " ideal model delta sigma weight residual 119.98 116.88 3.10 8.50e-01 1.38e+00 1.33e+01 angle pdb=" N BGLY A 586 " pdb=" CA BGLY A 586 " pdb=" C BGLY A 586 " ideal model delta sigma weight residual 113.18 120.66 -7.48 2.37e+00 1.78e-01 9.96e+00 angle pdb=" C AGLY C 586 " pdb=" N ASER C 587 " pdb=" CA ASER C 587 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.30e+00 ... (remaining 29987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 12043 17.73 - 35.46: 763 35.46 - 53.18: 102 53.18 - 70.91: 40 70.91 - 88.64: 16 Dihedral angle restraints: 12964 sinusoidal: 4835 harmonic: 8129 Sorted by residual: dihedral pdb=" CA ASER C 587 " pdb=" C ASER C 587 " pdb=" N AHIS C 588 " pdb=" CA AHIS C 588 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CB GLU A 454 " pdb=" CG GLU A 454 " pdb=" CD GLU A 454 " pdb=" OE1 GLU A 454 " ideal model delta sinusoidal sigma weight residual 0.00 88.64 -88.64 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 454 " pdb=" CG GLU B 454 " pdb=" CD GLU B 454 " pdb=" OE1 GLU B 454 " ideal model delta sinusoidal sigma weight residual 0.00 -88.63 88.63 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1869 0.027 - 0.054: 864 0.054 - 0.081: 301 0.081 - 0.107: 186 0.107 - 0.134: 110 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA VAL B 240 " pdb=" N VAL B 240 " pdb=" C VAL B 240 " pdb=" CB VAL B 240 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 314 " pdb=" N ILE A 314 " pdb=" C ILE A 314 " pdb=" CB ILE A 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE B 314 " pdb=" N ILE B 314 " pdb=" C ILE B 314 " pdb=" CB ILE B 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 3327 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 551 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO B 552 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 552 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 552 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 551 " -0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO D 552 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO D 552 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 552 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 551 " 0.048 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO A 552 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " 0.040 5.00e-02 4.00e+02 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3159 2.77 - 3.30: 17917 3.30 - 3.83: 32600 3.83 - 4.37: 38986 4.37 - 4.90: 72960 Nonbonded interactions: 165622 Sorted by model distance: nonbonded pdb=" OG SER C 308 " pdb=" OD1 ASP C 310 " model vdw 2.236 3.040 nonbonded pdb=" OG SER D 308 " pdb=" OD1 ASP D 310 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 308 " pdb=" OD1 ASP B 310 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 308 " pdb=" OD1 ASP A 310 " model vdw 2.317 3.040 nonbonded pdb=" O SER B 304 " pdb=" OG SER B 304 " model vdw 2.318 3.040 ... (remaining 165617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 38 or resid 40 through 127 or resid 129 through \ 156 or resid 158 through 179 or (resid 180 through 200 and (name N or name CA or \ name C or name O or name CB )) or resid 201 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 287 or (res \ id 288 and (name N or name CA or name C or name O or name CB )) or resid 289 thr \ ough 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) \ or resid 352 through 396 or (resid 397 and (name N or name CA or name C or name \ O or name CB )) or resid 398 through 492 or (resid 493 and (name N or name CA or \ name C or name O or name CB )) or resid 494 through 583 or resid 592 through 63 \ 7 or (resid 638 and (name N or name CA or name C or name O or name CB )) or resi \ d 639 through 731 or (resid 732 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'B' and (resid 9 through 38 or resid 40 through 48 or (resid 49 and (name \ N or name CA or name C or name O or name CB )) or resid 50 through 116 or (resi \ d 117 and (name N or name CA or name C or name O or name CB )) or resid 118 thro \ ugh 127 or resid 129 through 156 or resid 158 through 173 or (resid 174 and (nam \ e N or name CA or name C or name O or name CB )) or resid 175 through 217 or (re \ sid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 290 or (resid 291 and (name N or name CA or name C or name \ O or name CB or name CG )) or resid 292 through 492 or (resid 493 and (name N o \ r name CA or name C or name O or name CB )) or resid 494 through 574 or (resid 5 \ 75 and (name N or name CA or name C or name O or name CB )) or resid 576 through \ 583 or resid 592 through 637 or (resid 638 and (name N or name CA or name C or \ name O or name CB )) or resid 639 through 641 or (resid 642 and (name N or name \ CA or name C or name O or name CB )) or resid 643 through 693 or (resid 694 and \ (name N or name CA or name C or name O or name CB )) or resid 695 through 732)) selection = (chain 'C' and (resid 9 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 127 or resid 129 th \ rough 156 or resid 158 through 173 or (resid 174 and (name N or name CA or name \ C or name O or name CB )) or resid 175 through 179 or (resid 180 through 200 and \ (name N or name CA or name C or name O or name CB )) or resid 201 through 290 o \ r (resid 291 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 292 through 396 or (resid 397 and (name N or name CA or name C or name \ O or name CB )) or resid 398 through 492 or (resid 493 and (name N or name CA o \ r name C or name O or name CB )) or resid 494 through 574 or (resid 575 and (nam \ e N or name CA or name C or name O or name CB )) or resid 576 through 583 or res \ id 592 through 637 or (resid 638 and (name N or name CA or name C or name O or n \ ame CB )) or resid 639 through 641 or (resid 642 and (name N or name CA or name \ C or name O or name CB )) or resid 643 through 693 or (resid 694 and (name N or \ name CA or name C or name O or name CB )) or resid 695 through 731 or (resid 732 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 9 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 127 or resid 129 through 156 or res \ id 158 through 173 or (resid 174 and (name N or name CA or name C or name O or n \ ame CB )) or resid 175 through 179 or (resid 180 through 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 and \ (name N or name CA or name C or name O or name CB )) or resid 219 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 89 through 290 or (resid 291 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 292 through 350 or (resid 351 and (name N or name CA o \ r name C or name O or name CB )) or resid 352 through 396 or (resid 397 and (nam \ e N or name CA or name C or name O or name CB )) or resid 398 through 415 or (re \ sid 416 and (name N or name CA or name C or name O or name CB )) or resid 417 th \ rough 572 or (resid 573 through 575 and (name N or name CA or name C or name O o \ r name CB )) or resid 576 through 583 or resid 592 through 641 or (resid 642 and \ (name N or name CA or name C or name O or name CB )) or resid 643 through 693 o \ r (resid 694 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 95 through 731 or (resid 732 and (name N or name CA or name C or name O or name \ CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 2.970 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: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.830 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.002 0.057 21999 Z= 0.110 Angle : 0.521 7.479 29992 Z= 0.280 Chirality : 0.043 0.134 3330 Planarity : 0.005 0.106 3861 Dihedral : 12.521 88.637 7748 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 2808 helix: 0.66 (0.24), residues: 481 sheet: 0.90 (0.17), residues: 892 loop : -1.37 (0.14), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 417 TYR 0.009 0.001 TYR B 316 PHE 0.023 0.001 PHE A 514 TRP 0.012 0.001 TRP C 50 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00240 (21999) covalent geometry : angle 0.52149 (29992) hydrogen bonds : bond 0.18095 ( 793) hydrogen bonds : angle 6.36774 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: B 555 VAL cc_start: 0.8712 (t) cc_final: 0.8340 (m) REVERT: C 62 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7644 (mtp180) REVERT: D 684 MET cc_start: 0.8542 (mmm) cc_final: 0.8275 (tpp) REVERT: D 688 ARG cc_start: 0.7325 (mtp85) cc_final: 0.7106 (mtp85) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1425 time to fit residues: 45.5645 Evaluate side-chains 162 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN B 673 GLN C 673 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.109330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.085946 restraints weight = 116618.812| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 5.74 r_work: 0.2440 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21999 Z= 0.133 Angle : 0.552 8.603 29992 Z= 0.285 Chirality : 0.045 0.138 3330 Planarity : 0.005 0.078 3861 Dihedral : 3.910 24.987 3056 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.41 % Allowed : 3.71 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 2808 helix: 1.17 (0.23), residues: 493 sheet: 0.96 (0.17), residues: 894 loop : -1.35 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 417 TYR 0.010 0.001 TYR D 43 PHE 0.021 0.002 PHE A 514 TRP 0.012 0.001 TRP A 648 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00320 (21999) covalent geometry : angle 0.55218 (29992) hydrogen bonds : bond 0.04715 ( 793) hydrogen bonds : angle 5.03964 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: B 619 MET cc_start: 0.8495 (ttp) cc_final: 0.8214 (ttp) REVERT: B 624 ASP cc_start: 0.8913 (p0) cc_final: 0.8708 (p0) REVERT: C 619 MET cc_start: 0.8541 (ttp) cc_final: 0.8197 (ttp) outliers start: 8 outliers final: 7 residues processed: 164 average time/residue: 0.1474 time to fit residues: 37.9116 Evaluate side-chains 163 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 347 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN B 66 GLN C 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.106124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.083179 restraints weight = 132234.749| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 5.96 r_work: 0.2365 rms_B_bonded: 5.50 restraints_weight: 2.0000 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2354 r_free = 0.2354 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2354 r_free = 0.2354 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21999 Z= 0.232 Angle : 0.639 13.207 29992 Z= 0.329 Chirality : 0.049 0.148 3330 Planarity : 0.006 0.071 3861 Dihedral : 4.317 28.213 3056 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.54 % Allowed : 5.29 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 2808 helix: 1.07 (0.23), residues: 495 sheet: 0.75 (0.17), residues: 914 loop : -1.44 (0.14), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 57 TYR 0.010 0.002 TYR D 43 PHE 0.023 0.002 PHE A 514 TRP 0.015 0.001 TRP B 50 HIS 0.006 0.002 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00597 (21999) covalent geometry : angle 0.63909 (29992) hydrogen bonds : bond 0.05499 ( 793) hydrogen bonds : angle 5.02819 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.889 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 166 average time/residue: 0.1504 time to fit residues: 38.7309 Evaluate side-chains 160 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 695 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 88 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.108241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.085118 restraints weight = 128649.427| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 5.90 r_work: 0.2399 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21999 Z= 0.126 Angle : 0.541 10.864 29992 Z= 0.279 Chirality : 0.045 0.134 3330 Planarity : 0.005 0.066 3861 Dihedral : 4.073 27.003 3056 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.45 % Allowed : 6.02 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 2808 helix: 1.18 (0.23), residues: 501 sheet: 0.83 (0.17), residues: 906 loop : -1.39 (0.14), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 62 TYR 0.008 0.001 TYR D 43 PHE 0.020 0.001 PHE A 514 TRP 0.012 0.001 TRP D 124 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00304 (21999) covalent geometry : angle 0.54074 (29992) hydrogen bonds : bond 0.04188 ( 793) hydrogen bonds : angle 4.77284 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.788 Fit side-chains REVERT: C 619 MET cc_start: 0.8592 (ttp) cc_final: 0.8217 (ttp) outliers start: 9 outliers final: 8 residues processed: 165 average time/residue: 0.1554 time to fit residues: 39.8526 Evaluate side-chains 161 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 695 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 135 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN C 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.109179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.085861 restraints weight = 126320.208| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 6.04 r_work: 0.2418 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21999 Z= 0.110 Angle : 0.512 10.363 29992 Z= 0.264 Chirality : 0.044 0.133 3330 Planarity : 0.005 0.065 3861 Dihedral : 3.887 27.680 3056 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.77 % Allowed : 6.06 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 2808 helix: 1.39 (0.24), residues: 501 sheet: 0.94 (0.17), residues: 894 loop : -1.34 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.008 0.001 TYR D 43 PHE 0.018 0.001 PHE A 514 TRP 0.012 0.001 TRP B 50 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00262 (21999) covalent geometry : angle 0.51194 (29992) hydrogen bonds : bond 0.03735 ( 793) hydrogen bonds : angle 4.61196 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.782 Fit side-chains REVERT: C 619 MET cc_start: 0.8481 (ttp) cc_final: 0.8149 (ttp) REVERT: D 125 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7959 (tt0) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.1545 time to fit residues: 39.0828 Evaluate side-chains 164 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 695 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 178 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.105256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.082551 restraints weight = 125705.261| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 5.80 r_work: 0.2358 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2349 r_free = 0.2349 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2349 r_free = 0.2349 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 21999 Z= 0.245 Angle : 0.640 13.942 29992 Z= 0.330 Chirality : 0.050 0.153 3330 Planarity : 0.006 0.062 3861 Dihedral : 4.322 28.416 3056 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.00 % Allowed : 6.61 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 2808 helix: 1.14 (0.23), residues: 495 sheet: 0.73 (0.17), residues: 914 loop : -1.50 (0.14), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 57 TYR 0.011 0.002 TYR C 283 PHE 0.019 0.002 PHE D 591 TRP 0.011 0.001 TRP B 50 HIS 0.007 0.002 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00627 (21999) covalent geometry : angle 0.63988 (29992) hydrogen bonds : bond 0.05434 ( 793) hydrogen bonds : angle 4.89576 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.850 Fit side-chains REVERT: A 619 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8346 (ttp) REVERT: C 528 MET cc_start: 0.9408 (ttp) cc_final: 0.9205 (ttt) REVERT: D 125 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7979 (tp30) outliers start: 18 outliers final: 10 residues processed: 156 average time/residue: 0.1518 time to fit residues: 37.3821 Evaluate side-chains 155 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 695 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 65 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 276 optimal weight: 4.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN D 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.106813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.084012 restraints weight = 128306.415| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 5.94 r_work: 0.2382 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2373 r_free = 0.2373 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2373 r_free = 0.2373 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21999 Z= 0.148 Angle : 0.553 11.549 29992 Z= 0.287 Chirality : 0.046 0.145 3330 Planarity : 0.005 0.061 3861 Dihedral : 4.140 27.544 3056 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.81 % Allowed : 6.92 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 2808 helix: 1.22 (0.23), residues: 497 sheet: 0.75 (0.17), residues: 916 loop : -1.47 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 417 TYR 0.008 0.001 TYR D 43 PHE 0.018 0.002 PHE A 514 TRP 0.012 0.001 TRP D 124 HIS 0.004 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00368 (21999) covalent geometry : angle 0.55348 (29992) hydrogen bonds : bond 0.04367 ( 793) hydrogen bonds : angle 4.72883 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.836 Fit side-chains REVERT: A 619 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8331 (ttp) REVERT: C 619 MET cc_start: 0.8598 (ttp) cc_final: 0.8252 (ttp) REVERT: D 125 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7974 (tt0) outliers start: 14 outliers final: 10 residues processed: 156 average time/residue: 0.1684 time to fit residues: 41.0606 Evaluate side-chains 160 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 695 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 101 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.104197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.081509 restraints weight = 124815.070| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 5.62 r_work: 0.2345 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2335 r_free = 0.2335 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2335 r_free = 0.2335 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 21999 Z= 0.296 Angle : 0.685 14.928 29992 Z= 0.354 Chirality : 0.052 0.159 3330 Planarity : 0.006 0.060 3861 Dihedral : 4.531 29.187 3056 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.95 % Allowed : 7.24 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 2808 helix: 0.95 (0.23), residues: 493 sheet: 0.55 (0.17), residues: 928 loop : -1.66 (0.14), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 57 TYR 0.012 0.002 TYR A 43 PHE 0.021 0.002 PHE C 63 TRP 0.013 0.002 TRP D 648 HIS 0.008 0.002 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00763 (21999) covalent geometry : angle 0.68534 (29992) hydrogen bonds : bond 0.05925 ( 793) hydrogen bonds : angle 4.99876 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.826 Fit side-chains REVERT: A 619 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8394 (ttp) REVERT: C 62 ARG cc_start: 0.8732 (mtp85) cc_final: 0.8409 (mtp-110) REVERT: D 125 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8030 (tt0) outliers start: 17 outliers final: 11 residues processed: 151 average time/residue: 0.1617 time to fit residues: 38.8578 Evaluate side-chains 154 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 695 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 190 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 245 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.084946 restraints weight = 122625.326| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 5.84 r_work: 0.2404 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2396 r_free = 0.2396 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2396 r_free = 0.2396 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21999 Z= 0.119 Angle : 0.523 10.422 29992 Z= 0.272 Chirality : 0.044 0.134 3330 Planarity : 0.005 0.060 3861 Dihedral : 4.078 26.460 3056 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.72 % Allowed : 7.65 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 2808 helix: 1.24 (0.23), residues: 497 sheet: 0.74 (0.17), residues: 916 loop : -1.50 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 313 TYR 0.007 0.001 TYR D 316 PHE 0.018 0.001 PHE A 514 TRP 0.015 0.001 TRP D 124 HIS 0.003 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00289 (21999) covalent geometry : angle 0.52319 (29992) hydrogen bonds : bond 0.03847 ( 793) hydrogen bonds : angle 4.65199 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.831 Fit side-chains REVERT: C 402 THR cc_start: 0.9325 (m) cc_final: 0.9002 (p) REVERT: C 619 MET cc_start: 0.8555 (ttp) cc_final: 0.8250 (ttp) REVERT: D 125 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7994 (tt0) outliers start: 12 outliers final: 8 residues processed: 158 average time/residue: 0.1769 time to fit residues: 42.6805 Evaluate side-chains 159 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 618 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 131 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 233 optimal weight: 0.0010 chunk 95 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 222 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.107495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.084520 restraints weight = 129431.150| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 5.92 r_work: 0.2395 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2388 r_free = 0.2388 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2388 r_free = 0.2388 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21999 Z= 0.134 Angle : 0.537 11.102 29992 Z= 0.278 Chirality : 0.045 0.135 3330 Planarity : 0.005 0.060 3861 Dihedral : 4.031 28.124 3056 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.68 % Allowed : 7.74 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 2808 helix: 1.32 (0.23), residues: 497 sheet: 0.79 (0.17), residues: 906 loop : -1.51 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 688 TYR 0.008 0.001 TYR D 43 PHE 0.017 0.002 PHE A 514 TRP 0.012 0.001 TRP D 124 HIS 0.004 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00332 (21999) covalent geometry : angle 0.53729 (29992) hydrogen bonds : bond 0.04095 ( 793) hydrogen bonds : angle 4.63109 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.963 Fit side-chains REVERT: A 619 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8306 (ttp) REVERT: C 402 THR cc_start: 0.9319 (m) cc_final: 0.9018 (p) REVERT: C 619 MET cc_start: 0.8564 (ttp) cc_final: 0.8226 (ttp) REVERT: D 125 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7992 (tp30) outliers start: 11 outliers final: 9 residues processed: 155 average time/residue: 0.1672 time to fit residues: 40.2410 Evaluate side-chains 160 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 618 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 205 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 274 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.108089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.085048 restraints weight = 127422.494| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 5.87 r_work: 0.2403 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2396 r_free = 0.2396 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2396 r_free = 0.2396 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21999 Z= 0.119 Angle : 0.522 10.504 29992 Z= 0.271 Chirality : 0.044 0.133 3330 Planarity : 0.005 0.060 3861 Dihedral : 3.945 27.663 3056 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.77 % Allowed : 7.74 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 2808 helix: 1.34 (0.23), residues: 505 sheet: 0.78 (0.17), residues: 908 loop : -1.45 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 688 TYR 0.007 0.001 TYR D 43 PHE 0.017 0.001 PHE A 514 TRP 0.013 0.001 TRP C 50 HIS 0.003 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00289 (21999) covalent geometry : angle 0.52213 (29992) hydrogen bonds : bond 0.03831 ( 793) hydrogen bonds : angle 4.56914 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4238.19 seconds wall clock time: 73 minutes 23.79 seconds (4403.79 seconds total)