Starting phenix.real_space_refine on Sat Jul 4 15:43:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b0j_11968/07_2026/7b0j_11968.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b0j_11968/07_2026/7b0j_11968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7b0j_11968/07_2026/7b0j_11968.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b0j_11968/07_2026/7b0j_11968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b0j_11968/07_2026/7b0j_11968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b0j_11968/07_2026/7b0j_11968.map" model { file = "/net/cci-nas-00/data/ceres_data/7b0j_11968/07_2026/7b0j_11968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b0j_11968/07_2026/7b0j_11968.cif" } resolution = 2.85 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 14477 2.51 5 N 3644 2.21 5 O 3865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22102 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5480 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 656} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 5480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5480 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 656} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5482 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 25, 'TRANS': 656} Chain breaks: 4 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 5480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5480 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 656} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' CA': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' CA': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' CA': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' CA': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.00, per 1000 atoms: 0.18 Number of scatterers: 22102 At special positions: 0 Unit cell: (131.75, 131.75, 133.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 4 15.00 O 3865 8.00 N 3644 7.00 C 14477 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: 1.79 Conformation dependent library (CDL) restraints added in 983.1 milliseconds 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5248 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 4 sheets defined 75.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 165 removed outlier: 3.826A pdb=" N LYS A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.619A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 257 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.513A pdb=" N ASP A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 361 through 383 Processing helix chain 'A' and resid 400 through 423 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.741A pdb=" N ILE A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 457 Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 472 through 491 Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.611A pdb=" N LEU A 495 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 512 through 539 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.815A pdb=" N VAL A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 584 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 611 through 628 removed outlier: 3.660A pdb=" N HIS A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.747A pdb=" N ILE A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 removed outlier: 3.593A pdb=" N TRP A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 721 removed outlier: 3.540A pdb=" N ARG A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 727 removed outlier: 3.695A pdb=" N THR A 726 " --> pdb=" O ARG A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 removed outlier: 3.760A pdb=" N PHE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 165 removed outlier: 3.827A pdb=" N LYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.619A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 257 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 303 through 316 removed outlier: 3.513A pdb=" N ASP B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 361 through 383 Processing helix chain 'B' and resid 400 through 423 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 426 through 432 removed outlier: 3.740A pdb=" N ILE B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 457 Processing helix chain 'B' and resid 464 through 468 Processing helix chain 'B' and resid 472 through 491 Processing helix chain 'B' and resid 492 through 497 removed outlier: 3.610A pdb=" N LEU B 495 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 Processing helix chain 'B' and resid 512 through 539 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.815A pdb=" N VAL B 583 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 584 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 611 through 628 removed outlier: 3.661A pdb=" N HIS B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 Processing helix chain 'B' and resid 654 through 659 removed outlier: 3.747A pdb=" N ILE B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 674 removed outlier: 3.593A pdb=" N TRP B 672 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 721 removed outlier: 3.540A pdb=" N ARG B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 727 removed outlier: 3.695A pdb=" N THR B 726 " --> pdb=" O ARG B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 752 removed outlier: 3.761A pdb=" N PHE B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 165 removed outlier: 3.826A pdb=" N LYS C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.618A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 303 through 316 removed outlier: 3.512A pdb=" N ASP C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 339 Processing helix chain 'C' and resid 339 through 350 Processing helix chain 'C' and resid 361 through 383 Processing helix chain 'C' and resid 400 through 423 Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 426 through 432 removed outlier: 3.741A pdb=" N ILE C 430 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 457 Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 472 through 491 Processing helix chain 'C' and resid 492 through 497 removed outlier: 3.611A pdb=" N LEU C 495 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 512 through 539 Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 563 through 574 Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'C' and resid 580 through 585 removed outlier: 3.815A pdb=" N VAL C 583 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 584 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 611 through 628 removed outlier: 3.659A pdb=" N HIS C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 645 Processing helix chain 'C' and resid 654 through 659 removed outlier: 3.748A pdb=" N ILE C 659 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 674 removed outlier: 3.593A pdb=" N TRP C 672 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 721 removed outlier: 3.540A pdb=" N ARG C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 727 removed outlier: 3.695A pdb=" N THR C 726 " --> pdb=" O ARG C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 752 removed outlier: 3.760A pdb=" N PHE C 735 " --> pdb=" O THR C 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 108 through 116 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.827A pdb=" N LYS D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.617A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.513A pdb=" N ASP D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 339 through 350 Processing helix chain 'D' and resid 361 through 383 Processing helix chain 'D' and resid 400 through 423 Proline residue: D 408 - end of helix Processing helix chain 'D' and resid 426 through 432 removed outlier: 3.741A pdb=" N ILE D 430 " --> pdb=" O PHE D 426 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP D 432 " --> pdb=" O ASP D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 457 Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 472 through 491 Processing helix chain 'D' and resid 492 through 497 removed outlier: 3.610A pdb=" N LEU D 495 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 512 through 539 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 580 through 585 removed outlier: 3.814A pdb=" N VAL D 583 " --> pdb=" O SER D 580 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 584 " --> pdb=" O LEU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 611 through 628 removed outlier: 3.661A pdb=" N HIS D 626 " --> pdb=" O ASN D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 645 Processing helix chain 'D' and resid 654 through 659 removed outlier: 3.747A pdb=" N ILE D 659 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 674 removed outlier: 3.593A pdb=" N TRP D 672 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 721 removed outlier: 3.541A pdb=" N ARG D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 727 removed outlier: 3.696A pdb=" N THR D 726 " --> pdb=" O ARG D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 752 removed outlier: 3.761A pdb=" N PHE D 735 " --> pdb=" O THR D 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'D' and resid 66 through 67 1384 hydrogen bonds defined for protein. 4092 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: 3.07 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3437 1.30 - 1.43: 6291 1.43 - 1.56: 12722 1.56 - 1.68: 20 1.68 - 1.81: 176 Bond restraints: 22646 Sorted by residual: bond pdb=" O5 LPP A1001 " pdb=" P1 LPP A1001 " ideal model delta sigma weight residual 2.278 1.652 0.626 2.00e-02 2.50e+03 9.81e+02 bond pdb=" O5 LPP D1001 " pdb=" P1 LPP D1001 " ideal model delta sigma weight residual 2.278 1.652 0.626 2.00e-02 2.50e+03 9.81e+02 bond pdb=" O5 LPP C1001 " pdb=" P1 LPP C1001 " ideal model delta sigma weight residual 2.278 1.652 0.626 2.00e-02 2.50e+03 9.80e+02 bond pdb=" O5 LPP B1001 " pdb=" P1 LPP B1001 " ideal model delta sigma weight residual 2.278 1.653 0.625 2.00e-02 2.50e+03 9.78e+02 bond pdb=" O4 LPP C1001 " pdb=" P1 LPP C1001 " ideal model delta sigma weight residual 1.764 1.498 0.266 2.00e-02 2.50e+03 1.76e+02 ... (remaining 22641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.30: 30663 9.30 - 18.60: 24 18.60 - 27.90: 4 27.90 - 37.20: 8 37.20 - 46.49: 4 Bond angle restraints: 30703 Sorted by residual: angle pdb=" O4 LPP C1001 " pdb=" P1 LPP C1001 " pdb=" O5 LPP C1001 " ideal model delta sigma weight residual 62.99 109.48 -46.49 3.00e+00 1.11e-01 2.40e+02 angle pdb=" O4 LPP A1001 " pdb=" P1 LPP A1001 " pdb=" O5 LPP A1001 " ideal model delta sigma weight residual 62.99 109.46 -46.47 3.00e+00 1.11e-01 2.40e+02 angle pdb=" O4 LPP D1001 " pdb=" P1 LPP D1001 " pdb=" O5 LPP D1001 " ideal model delta sigma weight residual 62.99 109.45 -46.46 3.00e+00 1.11e-01 2.40e+02 angle pdb=" O4 LPP B1001 " pdb=" P1 LPP B1001 " pdb=" O5 LPP B1001 " ideal model delta sigma weight residual 62.99 109.40 -46.41 3.00e+00 1.11e-01 2.39e+02 angle pdb=" C6 LPP D1001 " pdb=" O5 LPP D1001 " pdb=" P1 LPP D1001 " ideal model delta sigma weight residual 82.33 118.98 -36.65 3.00e+00 1.11e-01 1.49e+02 ... (remaining 30698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11730 17.95 - 35.90: 1347 35.90 - 53.85: 296 53.85 - 71.79: 64 71.79 - 89.74: 28 Dihedral angle restraints: 13465 sinusoidal: 5397 harmonic: 8068 Sorted by residual: dihedral pdb=" CA ASN A 558 " pdb=" C ASN A 558 " pdb=" N ASN A 559 " pdb=" CA ASN A 559 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN D 558 " pdb=" C ASN D 558 " pdb=" N ASN D 559 " pdb=" CA ASN D 559 " ideal model delta harmonic sigma weight residual 180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASN B 558 " pdb=" C ASN B 558 " pdb=" N ASN B 559 " pdb=" CA ASN B 559 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 13462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2057 0.040 - 0.081: 1124 0.081 - 0.121: 197 0.121 - 0.161: 67 0.161 - 0.201: 8 Chirality restraints: 3453 Sorted by residual: chirality pdb=" CA PRO A 399 " pdb=" N PRO A 399 " pdb=" C PRO A 399 " pdb=" CB PRO A 399 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA PRO B 399 " pdb=" N PRO B 399 " pdb=" C PRO B 399 " pdb=" CB PRO B 399 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA PRO C 399 " pdb=" N PRO C 399 " pdb=" C PRO C 399 " pdb=" CB PRO C 399 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 3450 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 398 " 0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO A 399 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 398 " 0.056 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 399 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 399 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 399 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 398 " -0.056 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO C 399 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 399 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 399 " -0.046 5.00e-02 4.00e+02 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5540 2.79 - 3.32: 22200 3.32 - 3.85: 37220 3.85 - 4.37: 44469 4.37 - 4.90: 75861 Nonbonded interactions: 185290 Sorted by model distance: nonbonded pdb=" O LEU C 29 " pdb=" NZ LYS C 34 " model vdw 2.265 3.120 nonbonded pdb=" O LEU D 29 " pdb=" NZ LYS D 34 " model vdw 2.265 3.120 nonbonded pdb=" O LEU B 29 " pdb=" NZ LYS B 34 " model vdw 2.266 3.120 nonbonded pdb=" O LEU A 29 " pdb=" NZ LYS A 34 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG B 491 " pdb=" OG SER B 494 " model vdw 2.306 3.120 ... (remaining 185285 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' selection = chain 'B' selection = (chain 'C' and (resid 17 through 670 or (resid 671 and (name N or name CA or nam \ e C or name O or name CB )) or resid 672 through 1002)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.680 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 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 : 0.012 0.626 22646 Z= 0.575 Angle : 1.176 46.495 30703 Z= 0.515 Chirality : 0.048 0.201 3453 Planarity : 0.006 0.086 3804 Dihedral : 16.482 89.742 8217 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.03 % Allowed : 0.51 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.16), residues: 2688 helix: 0.90 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : -2.45 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 491 TYR 0.028 0.003 TYR D 155 PHE 0.030 0.003 PHE A 340 TRP 0.032 0.003 TRP A 326 HIS 0.008 0.002 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.01225 / 0.58 (22646) covalent geometry : angle 1.17636 / 0.51 (30703) hydrogen bonds : bond 0.12887 / 8.58 ( 1384) hydrogen bonds : angle 5.74742 / 4.12 ( 4092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 432 time to evaluate : 0.674 Fit side-chains REVERT: A 79 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7235 (mt-10) REVERT: A 98 ASP cc_start: 0.7502 (m-30) cc_final: 0.7292 (m-30) REVERT: A 676 HIS cc_start: 0.2274 (OUTLIER) cc_final: 0.1259 (p-80) REVERT: B 79 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7238 (mt-10) REVERT: B 98 ASP cc_start: 0.7499 (m-30) cc_final: 0.7282 (m-30) REVERT: B 676 HIS cc_start: 0.2311 (OUTLIER) cc_final: 0.1274 (p-80) REVERT: C 79 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7240 (mt-10) REVERT: C 98 ASP cc_start: 0.7486 (m-30) cc_final: 0.7275 (m-30) REVERT: C 676 HIS cc_start: 0.2387 (OUTLIER) cc_final: 0.1358 (p-80) REVERT: D 79 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7227 (mt-10) REVERT: D 98 ASP cc_start: 0.7500 (m-30) cc_final: 0.7285 (m-30) REVERT: D 676 HIS cc_start: 0.2272 (OUTLIER) cc_final: 0.1261 (p-80) outliers start: 24 outliers final: 4 residues processed: 448 average time/residue: 0.6174 time to fit residues: 313.5435 Evaluate side-chains 402 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 394 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 727 GLU Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain D residue 727 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN A 585 ASN B 308 GLN B 585 ASN C 308 GLN C 585 ASN D 308 GLN D 585 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123932 restraints weight = 24131.942| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.62 r_work: 0.3128 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22646 Z= 0.127 Angle : 0.539 7.109 30703 Z= 0.285 Chirality : 0.038 0.154 3453 Planarity : 0.005 0.054 3804 Dihedral : 8.657 81.321 3136 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.54 % Allowed : 11.19 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.17), residues: 2688 helix: 1.74 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -2.10 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 191 TYR 0.012 0.001 TYR A 459 PHE 0.027 0.002 PHE B 335 TRP 0.016 0.001 TRP A 326 HIS 0.002 0.000 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (22646) covalent geometry : angle 0.53851 / 0.28 (30703) hydrogen bonds : bond 0.04574 / 3.13 ( 1384) hydrogen bonds : angle 4.03467 / 2.90 ( 4092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 406 time to evaluate : 0.963 Fit side-chains REVERT: A 44 ASP cc_start: 0.7827 (t0) cc_final: 0.7262 (t0) REVERT: A 79 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7710 (mt-10) REVERT: A 98 ASP cc_start: 0.7712 (m-30) cc_final: 0.7507 (m-30) REVERT: A 228 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: A 522 ILE cc_start: 0.8616 (mt) cc_final: 0.8403 (mt) REVERT: A 589 ASP cc_start: 0.8651 (t0) cc_final: 0.8229 (t0) REVERT: A 615 MET cc_start: 0.8908 (mtt) cc_final: 0.8445 (mtt) REVERT: A 735 PHE cc_start: 0.8051 (t80) cc_final: 0.7810 (t80) REVERT: B 44 ASP cc_start: 0.7823 (t0) cc_final: 0.7262 (t0) REVERT: B 79 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7702 (mt-10) REVERT: B 98 ASP cc_start: 0.7724 (m-30) cc_final: 0.7520 (m-30) REVERT: B 228 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: B 522 ILE cc_start: 0.8621 (mt) cc_final: 0.8408 (mt) REVERT: B 589 ASP cc_start: 0.8661 (t0) cc_final: 0.8235 (t0) REVERT: B 615 MET cc_start: 0.8910 (mtt) cc_final: 0.8452 (mtt) REVERT: B 735 PHE cc_start: 0.8051 (t80) cc_final: 0.7808 (t80) REVERT: C 44 ASP cc_start: 0.7826 (t0) cc_final: 0.7265 (t0) REVERT: C 79 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 228 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: C 403 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6808 (tp30) REVERT: C 522 ILE cc_start: 0.8623 (mt) cc_final: 0.8403 (mt) REVERT: C 589 ASP cc_start: 0.8658 (t0) cc_final: 0.8245 (t0) REVERT: C 615 MET cc_start: 0.8914 (mtt) cc_final: 0.8458 (mtt) REVERT: C 735 PHE cc_start: 0.8052 (t80) cc_final: 0.7808 (t80) REVERT: D 44 ASP cc_start: 0.7812 (t0) cc_final: 0.7252 (t0) REVERT: D 79 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 98 ASP cc_start: 0.7721 (m-30) cc_final: 0.7515 (m-30) REVERT: D 228 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: D 522 ILE cc_start: 0.8626 (mt) cc_final: 0.8415 (mt) REVERT: D 589 ASP cc_start: 0.8649 (t0) cc_final: 0.8231 (t0) REVERT: D 615 MET cc_start: 0.8908 (mtt) cc_final: 0.8450 (mtt) REVERT: D 735 PHE cc_start: 0.8062 (t80) cc_final: 0.7809 (t80) outliers start: 36 outliers final: 0 residues processed: 414 average time/residue: 0.6018 time to fit residues: 286.7489 Evaluate side-chains 376 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 372 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain D residue 228 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 232 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 248 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125560 restraints weight = 24083.955| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.62 r_work: 0.3180 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22646 Z= 0.117 Angle : 0.506 6.481 30703 Z= 0.265 Chirality : 0.038 0.148 3453 Planarity : 0.004 0.046 3804 Dihedral : 7.270 54.995 3116 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.41 % Allowed : 16.25 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.17), residues: 2688 helix: 2.03 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.89 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.020 0.001 TYR B 624 PHE 0.019 0.001 PHE A 340 TRP 0.013 0.001 TRP C 314 HIS 0.002 0.000 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (22646) covalent geometry : angle 0.50620 / 0.27 (30703) hydrogen bonds : bond 0.04146 / 2.83 ( 1384) hydrogen bonds : angle 3.70031 / 2.67 ( 4092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 398 time to evaluate : 0.968 Fit side-chains REVERT: A 44 ASP cc_start: 0.7797 (t0) cc_final: 0.7210 (t0) REVERT: A 98 ASP cc_start: 0.7706 (m-30) cc_final: 0.7491 (m-30) REVERT: A 226 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7822 (mm-30) REVERT: A 228 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: A 229 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8048 (mt-10) REVERT: A 589 ASP cc_start: 0.8566 (t0) cc_final: 0.8148 (t0) REVERT: B 44 ASP cc_start: 0.7795 (t0) cc_final: 0.7249 (t0) REVERT: B 98 ASP cc_start: 0.7704 (m-30) cc_final: 0.7496 (m-30) REVERT: B 226 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7802 (mm-30) REVERT: B 228 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: B 496 PHE cc_start: 0.8198 (m-10) cc_final: 0.7863 (m-10) REVERT: B 589 ASP cc_start: 0.8574 (t0) cc_final: 0.8152 (t0) REVERT: B 619 MET cc_start: 0.8535 (mpt) cc_final: 0.8318 (mmt) REVERT: C 44 ASP cc_start: 0.7777 (t0) cc_final: 0.7232 (t0) REVERT: C 226 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7811 (mm-30) REVERT: C 228 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: C 496 PHE cc_start: 0.8208 (m-10) cc_final: 0.7877 (m-10) REVERT: C 589 ASP cc_start: 0.8567 (t0) cc_final: 0.8160 (t0) REVERT: C 619 MET cc_start: 0.8524 (mpt) cc_final: 0.8297 (mmt) REVERT: D 44 ASP cc_start: 0.7796 (t0) cc_final: 0.7217 (t0) REVERT: D 98 ASP cc_start: 0.7718 (m-30) cc_final: 0.7508 (m-30) REVERT: D 226 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7815 (mm-30) REVERT: D 228 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: D 229 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8042 (mt-10) REVERT: D 335 PHE cc_start: 0.7779 (t80) cc_final: 0.7578 (t80) REVERT: D 496 PHE cc_start: 0.8236 (m-10) cc_final: 0.7920 (m-10) REVERT: D 589 ASP cc_start: 0.8596 (t0) cc_final: 0.8169 (t0) outliers start: 33 outliers final: 4 residues processed: 413 average time/residue: 0.5763 time to fit residues: 273.8798 Evaluate side-chains 379 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 371 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 712 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 66 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 263 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 GLN A 308 GLN A 559 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 308 GLN B 559 ASN C 297 GLN C 308 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN D 308 GLN D 559 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.149789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117472 restraints weight = 24267.859| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.63 r_work: 0.3018 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 22646 Z= 0.297 Angle : 0.650 8.820 30703 Z= 0.333 Chirality : 0.044 0.163 3453 Planarity : 0.005 0.053 3804 Dihedral : 7.332 50.957 3116 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.96 % Allowed : 17.15 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.16), residues: 2688 helix: 1.67 (0.12), residues: 1904 sheet: None (None), residues: 0 loop : -2.10 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 511 TYR 0.020 0.002 TYR D 523 PHE 0.034 0.003 PHE B 335 TRP 0.017 0.002 TRP B 314 HIS 0.003 0.001 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.30 (22646) covalent geometry : angle 0.65004 / 0.33 (30703) hydrogen bonds : bond 0.05465 / 3.74 ( 1384) hydrogen bonds : angle 3.96645 / 2.86 ( 4092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 395 time to evaluate : 0.874 Fit side-chains REVERT: A 44 ASP cc_start: 0.7659 (t0) cc_final: 0.7046 (t0) REVERT: A 228 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A 229 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7894 (mt-10) REVERT: A 589 ASP cc_start: 0.8541 (t0) cc_final: 0.8092 (t0) REVERT: B 44 ASP cc_start: 0.7660 (t0) cc_final: 0.7052 (t0) REVERT: B 228 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: B 229 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7888 (mt-10) REVERT: B 589 ASP cc_start: 0.8528 (t0) cc_final: 0.8079 (t0) REVERT: C 44 ASP cc_start: 0.7628 (t0) cc_final: 0.7002 (t0) REVERT: C 228 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: C 229 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7889 (mt-10) REVERT: C 589 ASP cc_start: 0.8533 (t0) cc_final: 0.8097 (t0) REVERT: D 44 ASP cc_start: 0.7656 (t0) cc_final: 0.7044 (t0) REVERT: D 228 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: D 229 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7916 (mt-10) REVERT: D 589 ASP cc_start: 0.8517 (t0) cc_final: 0.8069 (t0) outliers start: 69 outliers final: 24 residues processed: 425 average time/residue: 0.5474 time to fit residues: 267.8518 Evaluate side-chains 407 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 379 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 339 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 712 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 110 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN A 559 ASN B 559 ASN D 308 GLN D 559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120837 restraints weight = 23860.456| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.70 r_work: 0.3080 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22646 Z= 0.128 Angle : 0.516 7.109 30703 Z= 0.269 Chirality : 0.038 0.159 3453 Planarity : 0.004 0.043 3804 Dihedral : 7.075 54.688 3116 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.23 % Allowed : 17.66 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.17), residues: 2688 helix: 1.98 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : -1.89 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.017 0.001 TYR D 200 PHE 0.026 0.002 PHE D 335 TRP 0.014 0.001 TRP D 635 HIS 0.002 0.000 HIS B 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (22646) covalent geometry : angle 0.51572 / 0.27 (30703) hydrogen bonds : bond 0.04275 / 2.92 ( 1384) hydrogen bonds : angle 3.70787 / 2.68 ( 4092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 398 time to evaluate : 0.797 Fit side-chains REVERT: A 44 ASP cc_start: 0.7818 (t0) cc_final: 0.7268 (t0) REVERT: A 228 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: A 229 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8161 (mt-10) REVERT: A 589 ASP cc_start: 0.8598 (t0) cc_final: 0.8192 (t0) REVERT: B 44 ASP cc_start: 0.7835 (t0) cc_final: 0.7261 (t0) REVERT: B 228 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: B 229 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8158 (mt-10) REVERT: B 589 ASP cc_start: 0.8593 (t0) cc_final: 0.8187 (t0) REVERT: C 44 ASP cc_start: 0.7827 (t0) cc_final: 0.7266 (t0) REVERT: C 228 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: C 229 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8152 (mt-10) REVERT: C 589 ASP cc_start: 0.8592 (t0) cc_final: 0.8194 (t0) REVERT: D 44 ASP cc_start: 0.7822 (t0) cc_final: 0.7273 (t0) REVERT: D 228 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: D 229 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8161 (mt-10) REVERT: D 496 PHE cc_start: 0.8354 (m-10) cc_final: 0.8146 (m-10) REVERT: D 589 ASP cc_start: 0.8573 (t0) cc_final: 0.8176 (t0) outliers start: 52 outliers final: 4 residues processed: 415 average time/residue: 0.5340 time to fit residues: 255.9301 Evaluate side-chains 377 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 369 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain D residue 228 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 128 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 249 optimal weight: 0.5980 chunk 201 optimal weight: 8.9990 chunk 268 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN A 420 GLN B 308 GLN D 308 GLN D 420 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121486 restraints weight = 24122.157| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.68 r_work: 0.3107 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22646 Z= 0.137 Angle : 0.508 7.242 30703 Z= 0.265 Chirality : 0.038 0.153 3453 Planarity : 0.004 0.043 3804 Dihedral : 7.004 55.924 3116 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.27 % Allowed : 18.47 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.17), residues: 2688 helix: 2.06 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -1.81 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.016 0.001 TYR A 200 PHE 0.031 0.002 PHE C 335 TRP 0.012 0.001 TRP D 635 HIS 0.002 0.000 HIS C 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (22646) covalent geometry : angle 0.50783 / 0.26 (30703) hydrogen bonds : bond 0.04246 / 2.90 ( 1384) hydrogen bonds : angle 3.65355 / 2.64 ( 4092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 379 time to evaluate : 0.909 Fit side-chains REVERT: A 44 ASP cc_start: 0.7845 (t0) cc_final: 0.7286 (t0) REVERT: A 228 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: A 229 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8150 (mt-10) REVERT: A 589 ASP cc_start: 0.8591 (t0) cc_final: 0.8203 (t0) REVERT: B 44 ASP cc_start: 0.7850 (t0) cc_final: 0.7296 (t0) REVERT: B 228 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: B 229 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8156 (mt-10) REVERT: B 589 ASP cc_start: 0.8575 (t0) cc_final: 0.8190 (t0) REVERT: C 44 ASP cc_start: 0.7847 (t0) cc_final: 0.7293 (t0) REVERT: C 228 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: C 229 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8154 (mt-10) REVERT: C 589 ASP cc_start: 0.8591 (t0) cc_final: 0.8207 (t0) REVERT: C 731 THR cc_start: 0.7671 (p) cc_final: 0.7470 (t) REVERT: D 44 ASP cc_start: 0.7848 (t0) cc_final: 0.7288 (t0) REVERT: D 228 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: D 229 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8159 (mt-10) REVERT: D 589 ASP cc_start: 0.8570 (t0) cc_final: 0.8190 (t0) REVERT: D 731 THR cc_start: 0.7661 (p) cc_final: 0.7457 (t) outliers start: 53 outliers final: 14 residues processed: 407 average time/residue: 0.6042 time to fit residues: 282.8413 Evaluate side-chains 390 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 372 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 712 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 46 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 159 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN B 222 GLN B 308 GLN B 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.155561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123966 restraints weight = 24069.574| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.63 r_work: 0.3141 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22646 Z= 0.114 Angle : 0.488 7.504 30703 Z= 0.254 Chirality : 0.037 0.182 3453 Planarity : 0.004 0.043 3804 Dihedral : 7.003 59.483 3116 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.49 % Allowed : 18.73 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.17), residues: 2688 helix: 2.18 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -1.70 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.014 0.001 TYR A 200 PHE 0.023 0.001 PHE D 335 TRP 0.013 0.001 TRP B 635 HIS 0.002 0.000 HIS B 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (22646) covalent geometry : angle 0.48845 / 0.25 (30703) hydrogen bonds : bond 0.03982 / 2.72 ( 1384) hydrogen bonds : angle 3.56554 / 2.58 ( 4092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 387 time to evaluate : 0.917 Fit side-chains REVERT: A 44 ASP cc_start: 0.7844 (t0) cc_final: 0.7278 (t0) REVERT: A 226 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7901 (mm-30) REVERT: A 228 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: A 229 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8133 (mt-10) REVERT: A 589 ASP cc_start: 0.8575 (t0) cc_final: 0.8144 (t0) REVERT: B 44 ASP cc_start: 0.7849 (t0) cc_final: 0.7286 (t0) REVERT: B 226 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7898 (mm-30) REVERT: B 228 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: B 229 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8144 (mt-10) REVERT: B 589 ASP cc_start: 0.8579 (t0) cc_final: 0.8146 (t0) REVERT: C 44 ASP cc_start: 0.7840 (t0) cc_final: 0.7273 (t0) REVERT: C 226 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7910 (mm-30) REVERT: C 228 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: C 229 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8139 (mt-10) REVERT: C 589 ASP cc_start: 0.8544 (t0) cc_final: 0.8117 (t0) REVERT: D 44 ASP cc_start: 0.7843 (t0) cc_final: 0.7278 (t0) REVERT: D 226 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7900 (mm-30) REVERT: D 228 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: D 229 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8151 (mt-10) REVERT: D 589 ASP cc_start: 0.8568 (t0) cc_final: 0.8135 (t0) outliers start: 58 outliers final: 12 residues processed: 416 average time/residue: 0.6071 time to fit residues: 290.8840 Evaluate side-chains 384 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 368 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 712 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 75 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 214 optimal weight: 0.0050 chunk 257 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 0.0060 chunk 93 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 250 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 ASN B 305 ASN C 305 ASN D 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.157543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126041 restraints weight = 23938.191| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.63 r_work: 0.3180 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22646 Z= 0.102 Angle : 0.478 8.112 30703 Z= 0.247 Chirality : 0.037 0.163 3453 Planarity : 0.004 0.042 3804 Dihedral : 6.955 57.689 3116 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.37 % Allowed : 20.70 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.17), residues: 2688 helix: 2.30 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -1.58 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.012 0.001 TYR A 200 PHE 0.032 0.001 PHE B 335 TRP 0.012 0.001 TRP B 635 HIS 0.002 0.000 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (22646) covalent geometry : angle 0.47815 / 0.25 (30703) hydrogen bonds : bond 0.03761 / 2.56 ( 1384) hydrogen bonds : angle 3.51123 / 2.54 ( 4092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 392 time to evaluate : 0.902 Fit side-chains REVERT: A 44 ASP cc_start: 0.7819 (t0) cc_final: 0.7279 (t0) REVERT: A 226 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7923 (mm-30) REVERT: A 228 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: A 229 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8092 (mt-10) REVERT: A 589 ASP cc_start: 0.8523 (t0) cc_final: 0.8161 (t0) REVERT: B 44 ASP cc_start: 0.7821 (t0) cc_final: 0.7276 (t0) REVERT: B 226 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7928 (mm-30) REVERT: B 228 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: B 229 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8110 (mt-10) REVERT: B 589 ASP cc_start: 0.8518 (t0) cc_final: 0.8153 (t0) REVERT: C 44 ASP cc_start: 0.7800 (t0) cc_final: 0.7248 (t0) REVERT: C 226 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7947 (mm-30) REVERT: C 228 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: C 229 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8104 (mt-10) REVERT: C 336 ILE cc_start: 0.8505 (mt) cc_final: 0.8223 (mm) REVERT: C 589 ASP cc_start: 0.8507 (t0) cc_final: 0.8144 (t0) REVERT: D 44 ASP cc_start: 0.7820 (t0) cc_final: 0.7278 (t0) REVERT: D 226 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7946 (mm-30) REVERT: D 228 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: D 229 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8119 (mt-10) REVERT: D 589 ASP cc_start: 0.8505 (t0) cc_final: 0.8141 (t0) outliers start: 32 outliers final: 9 residues processed: 412 average time/residue: 0.6186 time to fit residues: 292.7304 Evaluate side-chains 402 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 389 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 22 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 9 optimal weight: 0.0000 chunk 155 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 215 optimal weight: 0.1980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN B 308 GLN C 420 GLN C 559 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124672 restraints weight = 24119.575| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.63 r_work: 0.3150 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22646 Z= 0.122 Angle : 0.500 8.369 30703 Z= 0.256 Chirality : 0.037 0.180 3453 Planarity : 0.004 0.042 3804 Dihedral : 7.112 57.804 3116 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.37 % Allowed : 21.13 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.17), residues: 2688 helix: 2.26 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -1.56 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.012 0.001 TYR A 200 PHE 0.021 0.001 PHE D 335 TRP 0.012 0.001 TRP A 314 HIS 0.001 0.000 HIS D 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (22646) covalent geometry : angle 0.49992 / 0.26 (30703) hydrogen bonds : bond 0.04031 / 2.75 ( 1384) hydrogen bonds : angle 3.53647 / 2.55 ( 4092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 392 time to evaluate : 0.879 Fit side-chains REVERT: A 44 ASP cc_start: 0.7789 (t0) cc_final: 0.7224 (t0) REVERT: A 226 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7848 (mm-30) REVERT: A 228 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: A 229 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8051 (mt-10) REVERT: A 589 ASP cc_start: 0.8571 (t0) cc_final: 0.8203 (t0) REVERT: B 44 ASP cc_start: 0.7777 (t0) cc_final: 0.7209 (t0) REVERT: B 226 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7871 (mm-30) REVERT: B 228 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: B 229 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8069 (mt-10) REVERT: B 589 ASP cc_start: 0.8552 (t0) cc_final: 0.8183 (t0) REVERT: C 44 ASP cc_start: 0.7788 (t0) cc_final: 0.7221 (t0) REVERT: C 226 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7877 (mm-30) REVERT: C 228 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: C 229 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8066 (mt-10) REVERT: C 336 ILE cc_start: 0.8429 (mt) cc_final: 0.8152 (mm) REVERT: C 403 GLU cc_start: 0.6771 (tp30) cc_final: 0.6531 (tp30) REVERT: C 589 ASP cc_start: 0.8518 (t0) cc_final: 0.8159 (t0) REVERT: D 44 ASP cc_start: 0.7787 (t0) cc_final: 0.7219 (t0) REVERT: D 226 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7877 (mm-30) REVERT: D 228 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: D 229 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8065 (mt-10) REVERT: D 403 GLU cc_start: 0.6759 (tp30) cc_final: 0.6435 (tp30) REVERT: D 527 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9068 (tp) REVERT: D 589 ASP cc_start: 0.8553 (t0) cc_final: 0.8190 (t0) outliers start: 32 outliers final: 15 residues processed: 406 average time/residue: 0.6271 time to fit residues: 292.0260 Evaluate side-chains 406 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 386 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 161 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 241 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 GLN C 559 ASN D 308 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118813 restraints weight = 24316.580| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.73 r_work: 0.3078 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22646 Z= 0.185 Angle : 0.567 9.209 30703 Z= 0.289 Chirality : 0.040 0.220 3453 Planarity : 0.004 0.041 3804 Dihedral : 7.457 58.638 3116 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.37 % Allowed : 21.30 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.17), residues: 2688 helix: 2.10 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -1.67 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 196 TYR 0.015 0.002 TYR C 523 PHE 0.025 0.002 PHE B 335 TRP 0.013 0.001 TRP A 314 HIS 0.002 0.001 HIS C 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (22646) covalent geometry : angle 0.56663 / 0.29 (30703) hydrogen bonds : bond 0.04692 / 3.21 ( 1384) hydrogen bonds : angle 3.69392 / 2.66 ( 4092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 375 time to evaluate : 0.658 Fit side-chains REVERT: A 44 ASP cc_start: 0.7866 (t0) cc_final: 0.7288 (t0) REVERT: A 228 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: A 229 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8137 (mt-10) REVERT: A 589 ASP cc_start: 0.8620 (t0) cc_final: 0.8245 (t0) REVERT: A 731 THR cc_start: 0.7788 (p) cc_final: 0.7561 (t) REVERT: B 44 ASP cc_start: 0.7876 (t0) cc_final: 0.7306 (t0) REVERT: B 228 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: B 229 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8191 (mt-10) REVERT: B 589 ASP cc_start: 0.8641 (t0) cc_final: 0.8253 (t0) REVERT: C 44 ASP cc_start: 0.7882 (t0) cc_final: 0.7310 (t0) REVERT: C 228 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: C 229 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8160 (mt-10) REVERT: C 589 ASP cc_start: 0.8627 (t0) cc_final: 0.8228 (t0) REVERT: D 44 ASP cc_start: 0.7869 (t0) cc_final: 0.7293 (t0) REVERT: D 228 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: D 229 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8151 (mt-10) REVERT: D 403 GLU cc_start: 0.6895 (tp30) cc_final: 0.6654 (tp30) REVERT: D 527 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9121 (tp) REVERT: D 589 ASP cc_start: 0.8610 (t0) cc_final: 0.8238 (t0) outliers start: 32 outliers final: 18 residues processed: 394 average time/residue: 0.6119 time to fit residues: 277.7003 Evaluate side-chains 392 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 369 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 712 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 193 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 258 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 118 optimal weight: 0.0980 chunk 212 optimal weight: 4.9990 chunk 215 optimal weight: 0.0870 chunk 17 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN B 308 GLN C 308 GLN D 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126331 restraints weight = 24063.220| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.60 r_work: 0.3152 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22646 Z= 0.108 Angle : 0.491 8.672 30703 Z= 0.253 Chirality : 0.037 0.216 3453 Planarity : 0.004 0.042 3804 Dihedral : 7.291 56.851 3116 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.20 % Allowed : 21.73 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.84 (0.17), residues: 2688 helix: 2.30 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -1.54 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.014 0.001 TYR C 200 PHE 0.021 0.001 PHE A 335 TRP 0.015 0.001 TRP B 635 HIS 0.001 0.000 HIS C 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (22646) covalent geometry : angle 0.49145 / 0.25 (30703) hydrogen bonds : bond 0.03950 / 2.70 ( 1384) hydrogen bonds : angle 3.55759 / 2.57 ( 4092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8195.61 seconds wall clock time: 140 minutes 26.38 seconds (8426.38 seconds total)