Starting phenix.real_space_refine on Thu Sep 18 16:22:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrk_48557/09_2025/9mrk_48557.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrk_48557/09_2025/9mrk_48557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mrk_48557/09_2025/9mrk_48557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrk_48557/09_2025/9mrk_48557.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mrk_48557/09_2025/9mrk_48557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrk_48557/09_2025/9mrk_48557.map" } resolution = 3.62 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 11885 2.51 5 N 2967 2.21 5 O 3318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18298 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3223 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 401} Chain breaks: 1 Chain: "D" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3219 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.68, per 1000 atoms: 0.26 Number of scatterers: 18298 At special positions: 0 Unit cell: (116.4, 124.16, 147.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3318 8.00 N 2967 7.00 C 11885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 67 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 76 " distance=2.03 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: 1.57 Conformation dependent library (CDL) restraints added in 791.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 24 sheets defined 56.6% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.828A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.618A pdb=" N GLY A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.530A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.121A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.572A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 3.759A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 641 removed outlier: 4.294A pdb=" N GLU A 637 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASP A 638 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.585A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 4.207A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.683A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.539A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.788A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.471A pdb=" N GLU B 413 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.882A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.520A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.782A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 614 Processing helix chain 'B' and resid 620 through 625 removed outlier: 3.576A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 675 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 removed outlier: 4.436A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 818 removed outlier: 3.705A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.712A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.565A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 524 through 545 removed outlier: 4.536A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 532 " --> pdb=" O CYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.184A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.595A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 625 removed outlier: 3.837A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 675 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.644A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.923A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.073A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.789A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 removed outlier: 3.737A pdb=" N LEU D 415 " --> pdb=" O HIS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.056A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.661A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.734A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 614 removed outlier: 3.549A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 625 removed outlier: 3.561A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.524A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 675 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 removed outlier: 4.335A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 773 through 781 removed outlier: 4.622A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY D 779 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 780 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 818 removed outlier: 4.233A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 799 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.585A pdb=" N LEU E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 removed outlier: 3.994A pdb=" N ARG E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 123 removed outlier: 3.853A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 131 through 159 removed outlier: 3.949A pdb=" N LEU E 135 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 206 removed outlier: 3.850A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP E 202 " --> pdb=" O HIS E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 28 removed outlier: 3.552A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 104 through 124 removed outlier: 3.841A pdb=" N ILE F 108 " --> pdb=" O SER F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 159 removed outlier: 4.057A pdb=" N GLY F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN F 159 " --> pdb=" O TYR F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 207 removed outlier: 3.955A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 28 removed outlier: 3.727A pdb=" N LEU G 11 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 removed outlier: 3.752A pdb=" N ARG G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 123 removed outlier: 3.898A pdb=" N ILE G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 132 through 159 removed outlier: 3.614A pdb=" N ALA G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN G 159 " --> pdb=" O TYR G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 206 removed outlier: 3.840A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE G 187 " --> pdb=" O ALA G 183 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP G 202 " --> pdb=" O HIS G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 28 removed outlier: 3.583A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.853A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 159 removed outlier: 3.938A pdb=" N GLY H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER H 147 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN H 159 " --> pdb=" O TYR H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 204 removed outlier: 3.911A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE H 186 " --> pdb=" O GLY H 182 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 441 removed outlier: 6.482A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.461A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.004A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.514A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.472A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 441 removed outlier: 6.368A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 497 through 498 Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.389A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 removed outlier: 5.848A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 497 through 498 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.407A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 76 through 78 removed outlier: 3.624A pdb=" N SER E 174 " --> pdb=" O TYR E 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.643A pdb=" N SER F 174 " --> pdb=" O TYR F 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.648A pdb=" N SER G 174 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 76 through 78 removed outlier: 3.703A pdb=" N SER H 174 " --> pdb=" O TYR H 34 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2709 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: 3.22 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5616 1.34 - 1.46: 4586 1.46 - 1.58: 8280 1.58 - 1.70: 0 1.70 - 1.81: 208 Bond restraints: 18690 Sorted by residual: bond pdb=" CG1 ILE F 188 " pdb=" CD1 ILE F 188 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.90e+00 bond pdb=" CG1 ILE H 188 " pdb=" CD1 ILE H 188 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CA SER C 615 " pdb=" C SER C 615 " ideal model delta sigma weight residual 1.522 1.503 0.018 1.37e-02 5.33e+03 1.81e+00 bond pdb=" CG1 ILE E 188 " pdb=" CD1 ILE E 188 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.45e+00 bond pdb=" CG1 ILE G 188 " pdb=" CD1 ILE G 188 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 ... (remaining 18685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 24549 1.53 - 3.06: 566 3.06 - 4.59: 72 4.59 - 6.12: 20 6.12 - 7.65: 3 Bond angle restraints: 25210 Sorted by residual: angle pdb=" C PRO C 520 " pdb=" N LEU C 521 " pdb=" CA LEU C 521 " ideal model delta sigma weight residual 122.56 116.17 6.39 1.50e+00 4.44e-01 1.81e+01 angle pdb=" N ALA C 522 " pdb=" CA ALA C 522 " pdb=" C ALA C 522 " ideal model delta sigma weight residual 107.73 112.61 -4.88 1.34e+00 5.57e-01 1.33e+01 angle pdb=" N SER C 615 " pdb=" CA SER C 615 " pdb=" C SER C 615 " ideal model delta sigma weight residual 113.23 108.77 4.46 1.24e+00 6.50e-01 1.29e+01 angle pdb=" N SER A 615 " pdb=" CA SER A 615 " pdb=" C SER A 615 " ideal model delta sigma weight residual 113.23 108.83 4.40 1.24e+00 6.50e-01 1.26e+01 angle pdb=" N ASP A 519 " pdb=" CA ASP A 519 " pdb=" C ASP A 519 " ideal model delta sigma weight residual 109.81 117.46 -7.65 2.21e+00 2.05e-01 1.20e+01 ... (remaining 25205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10355 17.85 - 35.69: 503 35.69 - 53.54: 90 53.54 - 71.38: 16 71.38 - 89.23: 16 Dihedral angle restraints: 10980 sinusoidal: 4274 harmonic: 6706 Sorted by residual: dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 175.71 -82.71 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.06 -73.06 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CA ALA C 522 " pdb=" C ALA C 522 " pdb=" N TYR C 523 " pdb=" CA TYR C 523 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 10977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1817 0.037 - 0.073: 797 0.073 - 0.110: 164 0.110 - 0.147: 44 0.147 - 0.183: 4 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA THR A 744 " pdb=" N THR A 744 " pdb=" C THR A 744 " pdb=" CB THR A 744 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA PRO C 520 " pdb=" N PRO C 520 " pdb=" C PRO C 520 " pdb=" CB PRO C 520 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CG LEU D 610 " pdb=" CB LEU D 610 " pdb=" CD1 LEU D 610 " pdb=" CD2 LEU D 610 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 2823 not shown) Planarity restraints: 3106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 614 " 0.023 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C SER C 614 " -0.079 2.00e-02 2.50e+03 pdb=" O SER C 614 " 0.030 2.00e-02 2.50e+03 pdb=" N SER C 615 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 614 " -0.023 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C SER A 614 " 0.078 2.00e-02 2.50e+03 pdb=" O SER A 614 " -0.029 2.00e-02 2.50e+03 pdb=" N SER A 615 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 615 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C SER A 615 " -0.054 2.00e-02 2.50e+03 pdb=" O SER A 615 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 616 " 0.018 2.00e-02 2.50e+03 ... (remaining 3103 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3552 2.77 - 3.31: 18013 3.31 - 3.84: 27042 3.84 - 4.37: 30947 4.37 - 4.90: 54830 Nonbonded interactions: 134384 Sorted by model distance: nonbonded pdb=" OD1 ASP A 490 " pdb=" NZ LYS A 738 " model vdw 2.242 3.120 nonbonded pdb=" OD2 ASP D 638 " pdb=" NE2 GLN D 642 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLU A 710 " pdb=" OH TYR A 768 " model vdw 2.303 3.040 nonbonded pdb=" O PHE A 623 " pdb=" N THR A 625 " model vdw 2.313 3.120 nonbonded pdb=" NH1 ARG C 453 " pdb=" OD1 ASP C 456 " model vdw 2.357 3.120 ... (remaining 134379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 1301)) selection = (chain 'C' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 6.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.940 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.003 0.054 18702 Z= 0.144 Angle : 0.589 7.646 25234 Z= 0.341 Chirality : 0.042 0.183 2826 Planarity : 0.006 0.062 3106 Dihedral : 11.686 89.228 6668 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -1.34 (0.16), residues: 2298 helix: -0.62 (0.13), residues: 1204 sheet: -0.72 (0.41), residues: 144 loop : -1.09 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG B 660 TYR 0.017 0.002 TYR C 732 PHE 0.018 0.002 PHE G 140 TRP 0.024 0.002 TRP A 766 HIS 0.003 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00316 (18690) covalent geometry : angle 0.58845 (25210) SS BOND : bond 0.00143 ( 12) SS BOND : angle 0.68444 ( 24) hydrogen bonds : bond 0.17828 ( 947) hydrogen bonds : angle 5.77938 ( 2709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 SER cc_start: 0.8544 (p) cc_final: 0.8100 (m) REVERT: C 671 TRP cc_start: 0.8100 (t-100) cc_final: 0.7736 (t-100) REVERT: C 788 SER cc_start: 0.8557 (p) cc_final: 0.8088 (m) REVERT: D 498 LEU cc_start: 0.8434 (pt) cc_final: 0.7940 (pt) REVERT: F 202 ASP cc_start: 0.7841 (t0) cc_final: 0.6955 (m-30) REVERT: H 198 HIS cc_start: 0.7114 (t70) cc_final: 0.6874 (m-70) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.1728 time to fit residues: 132.4403 Evaluate side-chains 265 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 642 GLN A 714 GLN A 791 ASN C 791 ASN E 159 ASN H 198 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.176201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140450 restraints weight = 27805.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138633 restraints weight = 35237.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.140439 restraints weight = 34393.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142119 restraints weight = 21722.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142469 restraints weight = 20103.917| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18702 Z= 0.162 Angle : 0.613 8.011 25234 Z= 0.326 Chirality : 0.043 0.190 2826 Planarity : 0.004 0.062 3106 Dihedral : 4.609 49.973 2526 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 9.72 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 0.44 (0.18), residues: 2298 helix: 1.19 (0.15), residues: 1232 sheet: -0.21 (0.39), residues: 166 loop : -0.82 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 101 TYR 0.015 0.002 TYR B 421 PHE 0.023 0.002 PHE G 17 TRP 0.014 0.001 TRP C 605 HIS 0.005 0.001 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00380 (18690) covalent geometry : angle 0.60828 (25210) SS BOND : bond 0.00325 ( 12) SS BOND : angle 2.51885 ( 24) hydrogen bonds : bond 0.06115 ( 947) hydrogen bonds : angle 4.30817 ( 2709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 305 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: A 788 SER cc_start: 0.8378 (p) cc_final: 0.8146 (m) REVERT: B 405 TYR cc_start: 0.7637 (m-80) cc_final: 0.7432 (m-10) REVERT: C 788 SER cc_start: 0.8420 (p) cc_final: 0.8150 (m) REVERT: D 594 ARG cc_start: 0.7599 (ptm160) cc_final: 0.7319 (ttp-110) REVERT: F 188 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8919 (mp) REVERT: H 188 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8869 (mp) outliers start: 55 outliers final: 31 residues processed: 349 average time/residue: 0.1564 time to fit residues: 79.9044 Evaluate side-chains 285 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 211 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 HIS H 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.169362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135462 restraints weight = 27941.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138594 restraints weight = 48591.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139309 restraints weight = 29045.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.140486 restraints weight = 19902.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140840 restraints weight = 17039.123| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18702 Z= 0.216 Angle : 0.648 11.314 25234 Z= 0.343 Chirality : 0.044 0.181 2826 Planarity : 0.005 0.051 3106 Dihedral : 4.655 44.032 2526 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 4.04 % Allowed : 12.79 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 0.60 (0.18), residues: 2298 helix: 1.52 (0.15), residues: 1232 sheet: -0.30 (0.44), residues: 134 loop : -1.01 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 98 TYR 0.018 0.002 TYR D 702 PHE 0.019 0.002 PHE A 623 TRP 0.019 0.002 TRP A 578 HIS 0.007 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00519 (18690) covalent geometry : angle 0.64611 (25210) SS BOND : bond 0.00455 ( 12) SS BOND : angle 1.73322 ( 24) hydrogen bonds : bond 0.07089 ( 947) hydrogen bonds : angle 4.32979 ( 2709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 278 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 721 MET cc_start: 0.7761 (ppp) cc_final: 0.7537 (ppp) REVERT: C 629 MET cc_start: 0.7170 (mmm) cc_final: 0.6115 (tmm) REVERT: D 756 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: F 64 ARG cc_start: 0.6564 (ptp-110) cc_final: 0.6043 (ptp-110) REVERT: F 188 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8881 (mp) REVERT: F 202 ASP cc_start: 0.7601 (t70) cc_final: 0.6952 (m-30) REVERT: H 31 TYR cc_start: 0.7857 (m-80) cc_final: 0.7559 (m-10) REVERT: H 188 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8880 (mp) outliers start: 79 outliers final: 57 residues processed: 342 average time/residue: 0.1498 time to fit residues: 75.7084 Evaluate side-chains 302 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 217 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 214 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS E 59 HIS E 131 HIS F 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.172143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139158 restraints weight = 27639.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138883 restraints weight = 41589.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.140641 restraints weight = 35947.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141551 restraints weight = 23115.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142556 restraints weight = 19826.699| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18702 Z= 0.153 Angle : 0.563 8.386 25234 Z= 0.297 Chirality : 0.041 0.167 2826 Planarity : 0.004 0.044 3106 Dihedral : 4.274 35.754 2526 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 3.68 % Allowed : 14.42 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 0.83 (0.18), residues: 2298 helix: 1.84 (0.15), residues: 1234 sheet: -0.56 (0.40), residues: 148 loop : -1.08 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 98 TYR 0.014 0.001 TYR D 421 PHE 0.013 0.002 PHE G 17 TRP 0.012 0.001 TRP C 578 HIS 0.004 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00358 (18690) covalent geometry : angle 0.56218 (25210) SS BOND : bond 0.00304 ( 12) SS BOND : angle 1.29233 ( 24) hydrogen bonds : bond 0.05694 ( 947) hydrogen bonds : angle 3.99229 ( 2709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 250 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 TYR cc_start: 0.7776 (m-80) cc_final: 0.7568 (m-10) REVERT: B 721 MET cc_start: 0.7859 (ppp) cc_final: 0.7610 (ppp) REVERT: B 756 GLN cc_start: 0.7604 (mp10) cc_final: 0.7198 (mp10) REVERT: D 587 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: F 31 TYR cc_start: 0.7861 (m-80) cc_final: 0.7512 (m-10) REVERT: F 188 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8817 (mp) REVERT: G 9 MET cc_start: 0.5776 (tpt) cc_final: 0.5450 (tpp) REVERT: H 31 TYR cc_start: 0.7864 (m-80) cc_final: 0.7497 (m-10) REVERT: H 64 ARG cc_start: 0.6663 (ptp-110) cc_final: 0.6187 (ptp-110) REVERT: H 188 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8781 (mp) outliers start: 72 outliers final: 48 residues processed: 310 average time/residue: 0.1437 time to fit residues: 66.2603 Evaluate side-chains 285 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 587 GLN Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 0.0970 chunk 188 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.168309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133308 restraints weight = 27500.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135556 restraints weight = 44621.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136642 restraints weight = 31896.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.137705 restraints weight = 20783.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138098 restraints weight = 18911.406| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18702 Z= 0.170 Angle : 0.578 9.285 25234 Z= 0.304 Chirality : 0.042 0.166 2826 Planarity : 0.004 0.046 3106 Dihedral : 4.218 39.107 2526 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 4.25 % Allowed : 15.35 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 0.76 (0.18), residues: 2298 helix: 1.83 (0.15), residues: 1240 sheet: -0.63 (0.39), residues: 160 loop : -1.21 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 98 TYR 0.016 0.001 TYR A 533 PHE 0.016 0.002 PHE A 546 TRP 0.014 0.001 TRP C 578 HIS 0.004 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00404 (18690) covalent geometry : angle 0.57719 (25210) SS BOND : bond 0.00307 ( 12) SS BOND : angle 1.23837 ( 24) hydrogen bonds : bond 0.06231 ( 947) hydrogen bonds : angle 4.05113 ( 2709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 241 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.7124 (ttm) cc_final: 0.6877 (ttp) REVERT: A 816 TYR cc_start: 0.7145 (t80) cc_final: 0.6939 (t80) REVERT: B 721 MET cc_start: 0.7816 (ppp) cc_final: 0.7584 (ppp) REVERT: B 756 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: D 756 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: E 31 TYR cc_start: 0.7939 (m-80) cc_final: 0.7630 (m-80) REVERT: F 31 TYR cc_start: 0.7945 (m-80) cc_final: 0.7591 (m-10) REVERT: F 188 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8846 (mp) REVERT: G 9 MET cc_start: 0.5862 (tpt) cc_final: 0.5518 (tpp) REVERT: H 31 TYR cc_start: 0.7891 (m-80) cc_final: 0.7607 (m-10) REVERT: H 64 ARG cc_start: 0.6667 (ptp-110) cc_final: 0.6175 (ptp-110) REVERT: H 188 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8810 (mp) outliers start: 83 outliers final: 60 residues processed: 308 average time/residue: 0.1409 time to fit residues: 65.7825 Evaluate side-chains 293 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 229 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 33 optimal weight: 0.0970 chunk 137 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 79 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.173973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141269 restraints weight = 27497.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.141148 restraints weight = 37823.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142147 restraints weight = 36979.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143030 restraints weight = 22057.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143409 restraints weight = 19348.142| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18702 Z= 0.113 Angle : 0.521 9.605 25234 Z= 0.272 Chirality : 0.040 0.154 2826 Planarity : 0.004 0.041 3106 Dihedral : 3.917 32.518 2526 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 3.07 % Allowed : 16.52 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.07 (0.18), residues: 2298 helix: 2.12 (0.15), residues: 1244 sheet: -0.58 (0.39), residues: 160 loop : -1.14 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.010 0.001 TYR A 700 PHE 0.010 0.001 PHE G 17 TRP 0.011 0.001 TRP G 177 HIS 0.003 0.000 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00248 (18690) covalent geometry : angle 0.52025 (25210) SS BOND : bond 0.00145 ( 12) SS BOND : angle 0.94843 ( 24) hydrogen bonds : bond 0.04710 ( 947) hydrogen bonds : angle 3.73414 ( 2709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 252 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 TYR cc_start: 0.7022 (t80) cc_final: 0.6746 (t80) REVERT: B 756 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: D 756 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: E 9 MET cc_start: 0.5248 (tpt) cc_final: 0.4743 (tpp) REVERT: F 31 TYR cc_start: 0.7894 (m-80) cc_final: 0.7539 (m-10) REVERT: F 188 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8788 (mp) REVERT: G 9 MET cc_start: 0.5566 (tpt) cc_final: 0.5291 (tpp) REVERT: H 31 TYR cc_start: 0.7867 (m-80) cc_final: 0.7512 (m-10) REVERT: H 64 ARG cc_start: 0.6508 (ptp-110) cc_final: 0.6263 (ptp-110) REVERT: H 188 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8745 (mp) outliers start: 60 outliers final: 40 residues processed: 300 average time/residue: 0.1442 time to fit residues: 64.8907 Evaluate side-chains 282 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 158 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 18 optimal weight: 0.0370 chunk 173 optimal weight: 0.0040 chunk 11 optimal weight: 7.9990 chunk 230 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.172787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139911 restraints weight = 27542.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139538 restraints weight = 40115.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140856 restraints weight = 37177.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142044 restraints weight = 22774.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142599 restraints weight = 19416.703| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18702 Z= 0.110 Angle : 0.529 8.646 25234 Z= 0.273 Chirality : 0.040 0.181 2826 Planarity : 0.004 0.039 3106 Dihedral : 3.753 32.101 2526 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.35 % Rotamer: Outliers : 2.86 % Allowed : 17.08 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.28 (0.18), residues: 2298 helix: 2.29 (0.15), residues: 1234 sheet: -0.54 (0.38), residues: 184 loop : -0.99 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 98 TYR 0.013 0.001 TYR A 647 PHE 0.019 0.001 PHE H 72 TRP 0.014 0.001 TRP G 177 HIS 0.003 0.000 HIS H 81 Details of bonding type rmsd covalent geometry : bond 0.00240 (18690) covalent geometry : angle 0.52853 (25210) SS BOND : bond 0.00158 ( 12) SS BOND : angle 0.84656 ( 24) hydrogen bonds : bond 0.04442 ( 947) hydrogen bonds : angle 3.64922 ( 2709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 TYR cc_start: 0.6996 (t80) cc_final: 0.6717 (t80) REVERT: B 405 TYR cc_start: 0.7750 (m-80) cc_final: 0.7530 (m-10) REVERT: B 756 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: D 756 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: F 31 TYR cc_start: 0.7871 (m-80) cc_final: 0.7514 (m-10) REVERT: F 188 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8773 (mp) REVERT: G 9 MET cc_start: 0.5502 (tpt) cc_final: 0.5231 (tpp) REVERT: H 31 TYR cc_start: 0.7875 (m-80) cc_final: 0.7649 (m-10) REVERT: H 188 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8737 (mp) outliers start: 56 outliers final: 40 residues processed: 295 average time/residue: 0.1464 time to fit residues: 65.2853 Evaluate side-chains 278 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 222 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.168574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133374 restraints weight = 27641.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.135060 restraints weight = 38861.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136131 restraints weight = 32024.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137303 restraints weight = 20092.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139101 restraints weight = 17780.280| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18702 Z= 0.170 Angle : 0.591 9.488 25234 Z= 0.309 Chirality : 0.042 0.170 2826 Planarity : 0.004 0.057 3106 Dihedral : 4.009 39.346 2526 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 3.32 % Allowed : 17.03 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.02 (0.18), residues: 2298 helix: 2.10 (0.15), residues: 1236 sheet: -0.44 (0.40), residues: 160 loop : -1.18 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 98 TYR 0.015 0.001 TYR A 533 PHE 0.031 0.002 PHE F 72 TRP 0.014 0.001 TRP C 578 HIS 0.003 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00403 (18690) covalent geometry : angle 0.59052 (25210) SS BOND : bond 0.00249 ( 12) SS BOND : angle 0.97836 ( 24) hydrogen bonds : bond 0.06072 ( 947) hydrogen bonds : angle 3.90996 ( 2709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8168 (t) REVERT: B 756 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: C 816 TYR cc_start: 0.7068 (t80) cc_final: 0.6852 (t80) REVERT: D 756 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: D 767 TRP cc_start: 0.8462 (OUTLIER) cc_final: 0.8241 (m-90) REVERT: F 31 TYR cc_start: 0.7917 (m-80) cc_final: 0.7571 (m-10) REVERT: F 188 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8797 (mp) REVERT: G 9 MET cc_start: 0.5819 (tpt) cc_final: 0.5483 (tpp) REVERT: H 31 TYR cc_start: 0.7870 (m-80) cc_final: 0.7596 (m-10) REVERT: H 188 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8781 (mp) outliers start: 65 outliers final: 50 residues processed: 291 average time/residue: 0.1325 time to fit residues: 58.7528 Evaluate side-chains 286 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136467 restraints weight = 27477.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136330 restraints weight = 33866.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138003 restraints weight = 37382.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138729 restraints weight = 22587.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140266 restraints weight = 20008.605| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18702 Z= 0.123 Angle : 0.547 9.418 25234 Z= 0.283 Chirality : 0.040 0.203 2826 Planarity : 0.004 0.049 3106 Dihedral : 3.843 34.691 2526 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 2.81 % Allowed : 17.60 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.16 (0.18), residues: 2298 helix: 2.24 (0.15), residues: 1236 sheet: -0.46 (0.40), residues: 160 loop : -1.15 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.013 0.001 TYR C 647 PHE 0.012 0.001 PHE H 72 TRP 0.013 0.001 TRP G 177 HIS 0.003 0.000 HIS E 59 Details of bonding type rmsd covalent geometry : bond 0.00280 (18690) covalent geometry : angle 0.54714 (25210) SS BOND : bond 0.00154 ( 12) SS BOND : angle 0.81935 ( 24) hydrogen bonds : bond 0.04875 ( 947) hydrogen bonds : angle 3.68502 ( 2709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7956 (t) REVERT: A 714 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6674 (tm-30) REVERT: B 405 TYR cc_start: 0.7839 (m-80) cc_final: 0.7567 (m-10) REVERT: B 756 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: C 816 TYR cc_start: 0.6994 (t80) cc_final: 0.6755 (t80) REVERT: D 756 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7414 (mp10) REVERT: D 767 TRP cc_start: 0.8447 (OUTLIER) cc_final: 0.8211 (m-90) REVERT: E 9 MET cc_start: 0.5205 (tpt) cc_final: 0.4750 (tpp) REVERT: F 31 TYR cc_start: 0.7892 (m-80) cc_final: 0.7557 (m-10) REVERT: F 188 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8766 (mp) REVERT: G 9 MET cc_start: 0.5613 (tpt) cc_final: 0.5294 (tpp) REVERT: H 31 TYR cc_start: 0.7851 (m-80) cc_final: 0.7592 (m-10) REVERT: H 188 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8740 (mp) outliers start: 55 outliers final: 48 residues processed: 279 average time/residue: 0.1294 time to fit residues: 55.2369 Evaluate side-chains 280 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 150 optimal weight: 5.9990 chunk 118 optimal weight: 0.0070 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.170989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137942 restraints weight = 27678.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137574 restraints weight = 39216.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138794 restraints weight = 37730.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140205 restraints weight = 22631.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140685 restraints weight = 19118.332| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18702 Z= 0.125 Angle : 0.561 10.221 25234 Z= 0.289 Chirality : 0.040 0.185 2826 Planarity : 0.004 0.041 3106 Dihedral : 3.816 35.099 2526 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Rotamer: Outliers : 2.92 % Allowed : 17.49 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.18 (0.18), residues: 2298 helix: 2.28 (0.15), residues: 1236 sheet: -0.50 (0.42), residues: 148 loop : -1.16 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 98 TYR 0.015 0.001 TYR A 673 PHE 0.049 0.001 PHE F 72 TRP 0.011 0.001 TRP C 671 HIS 0.003 0.000 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00284 (18690) covalent geometry : angle 0.55995 (25210) SS BOND : bond 0.00280 ( 12) SS BOND : angle 1.11310 ( 24) hydrogen bonds : bond 0.04875 ( 947) hydrogen bonds : angle 3.65971 ( 2709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 VAL cc_start: 0.8206 (OUTLIER) cc_final: 0.7932 (t) REVERT: A 714 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6715 (tm-30) REVERT: B 405 TYR cc_start: 0.7810 (m-80) cc_final: 0.7558 (m-10) REVERT: B 756 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: C 816 TYR cc_start: 0.7025 (t80) cc_final: 0.6781 (t80) REVERT: D 756 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: D 767 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.8141 (m-90) REVERT: E 9 MET cc_start: 0.5301 (tpt) cc_final: 0.4820 (tpp) REVERT: F 31 TYR cc_start: 0.7853 (m-80) cc_final: 0.7517 (m-10) REVERT: F 188 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8776 (mp) REVERT: G 9 MET cc_start: 0.5597 (tpt) cc_final: 0.5277 (tpp) REVERT: H 31 TYR cc_start: 0.7882 (m-80) cc_final: 0.7619 (m-10) REVERT: H 188 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8739 (mp) outliers start: 57 outliers final: 49 residues processed: 281 average time/residue: 0.1337 time to fit residues: 56.6162 Evaluate side-chains 281 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 39 CYS Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 CYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 18 optimal weight: 1.9990 chunk 141 optimal weight: 0.2980 chunk 140 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134448 restraints weight = 27602.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135998 restraints weight = 41305.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137433 restraints weight = 34978.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137956 restraints weight = 22457.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139475 restraints weight = 19392.838| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18702 Z= 0.143 Angle : 0.578 10.201 25234 Z= 0.299 Chirality : 0.041 0.180 2826 Planarity : 0.004 0.041 3106 Dihedral : 3.885 37.301 2526 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 2.97 % Allowed : 17.60 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.09 (0.18), residues: 2298 helix: 2.20 (0.15), residues: 1236 sheet: -0.55 (0.42), residues: 148 loop : -1.21 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 36 TYR 0.018 0.001 TYR A 700 PHE 0.035 0.001 PHE F 72 TRP 0.010 0.001 TRP C 578 HIS 0.004 0.000 HIS E 59 Details of bonding type rmsd covalent geometry : bond 0.00336 (18690) covalent geometry : angle 0.57758 (25210) SS BOND : bond 0.00255 ( 12) SS BOND : angle 1.09596 ( 24) hydrogen bonds : bond 0.05386 ( 947) hydrogen bonds : angle 3.76150 ( 2709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.55 seconds wall clock time: 48 minutes 12.57 seconds (2892.57 seconds total)