Starting phenix.real_space_refine on Mon May 19 08:57:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrk_48557/05_2025/9mrk_48557.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrk_48557/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mrk_48557/05_2025/9mrk_48557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrk_48557/05_2025/9mrk_48557.map" model { file = "/net/cci-nas-00/data/ceres_data/9mrk_48557/05_2025/9mrk_48557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrk_48557/05_2025/9mrk_48557.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.44, per 1000 atoms: 0.63 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: 4.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.41 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: 5.34 Time building geometry restraints manager: 4.99 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 819 or resid 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: 4.390 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: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 40.750 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.590 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.16), 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 TRP 0.024 0.002 TRP A 766 HIS 0.003 0.001 HIS E 131 PHE 0.018 0.002 PHE G 140 TYR 0.017 0.002 TYR C 732 ARG 0.015 0.003 ARG B 660 Details of bonding type rmsd hydrogen bonds : bond 0.17828 ( 947) hydrogen bonds : angle 5.77938 ( 2709) SS BOND : bond 0.00143 ( 12) SS BOND : angle 0.68444 ( 24) covalent geometry : bond 0.00316 (18690) covalent geometry : angle 0.58845 (25210) *********************** 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 : 2.032 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: 0.3514 time to fit residues: 267.5273 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 : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 135 optimal weight: 0.0770 chunk 210 optimal weight: 2.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.175071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139590 restraints weight = 27826.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138848 restraints weight = 35806.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140478 restraints weight = 35088.604| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18702 Z= 0.170 Angle : 0.623 8.708 25234 Z= 0.331 Chirality : 0.043 0.191 2826 Planarity : 0.004 0.061 3106 Dihedral : 4.651 50.890 2526 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer: Outliers : 2.86 % Allowed : 9.77 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2298 helix: 1.16 (0.15), residues: 1234 sheet: -0.18 (0.39), residues: 166 loop : -0.82 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 605 HIS 0.005 0.001 HIS H 198 PHE 0.024 0.002 PHE G 17 TYR 0.015 0.002 TYR A 647 ARG 0.008 0.001 ARG F 101 Details of bonding type rmsd hydrogen bonds : bond 0.06251 ( 947) hydrogen bonds : angle 4.35313 ( 2709) SS BOND : bond 0.00444 ( 12) SS BOND : angle 2.41091 ( 24) covalent geometry : bond 0.00401 (18690) covalent geometry : angle 0.61873 (25210) *********************** 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: 56 poor density : 304 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6832 (tt0) REVERT: A 788 SER cc_start: 0.8424 (p) cc_final: 0.8195 (m) REVERT: C 788 SER cc_start: 0.8454 (p) cc_final: 0.8196 (m) REVERT: D 594 ARG cc_start: 0.7605 (ptm160) cc_final: 0.7297 (ttp-110) REVERT: F 64 ARG cc_start: 0.6546 (ptp-110) cc_final: 0.6208 (ptp-110) REVERT: F 188 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8929 (mp) REVERT: F 206 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6916 (tp-100) REVERT: H 188 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8884 (mp) outliers start: 56 outliers final: 30 residues processed: 348 average time/residue: 0.3254 time to fit residues: 165.6120 Evaluate side-chains 288 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 2.036 ------------------------------------------------------------------------------- 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 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 29 THR Chi-restraints excluded: chain E residue 121 ILE 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 180 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 187 optimal weight: 0.0770 chunk 148 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 188 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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** D 709 ASN H 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141843 restraints weight = 27629.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140754 restraints weight = 34843.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142270 restraints weight = 35527.368| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18702 Z= 0.131 Angle : 0.543 6.923 25234 Z= 0.287 Chirality : 0.040 0.174 2826 Planarity : 0.004 0.049 3106 Dihedral : 4.230 42.353 2526 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.35 % Rotamer: Outliers : 2.86 % Allowed : 12.99 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2298 helix: 1.79 (0.15), residues: 1246 sheet: -0.29 (0.38), residues: 184 loop : -0.91 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 671 HIS 0.003 0.001 HIS F 198 PHE 0.017 0.001 PHE G 17 TYR 0.014 0.001 TYR B 421 ARG 0.007 0.001 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.05251 ( 947) hydrogen bonds : angle 3.94751 ( 2709) SS BOND : bond 0.00213 ( 12) SS BOND : angle 1.48072 ( 24) covalent geometry : bond 0.00296 (18690) covalent geometry : angle 0.54109 (25210) *********************** 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 337 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6772 (tt0) REVERT: A 788 SER cc_start: 0.8372 (p) cc_final: 0.8168 (m) REVERT: B 721 MET cc_start: 0.7856 (ppp) cc_final: 0.7564 (ppp) REVERT: B 756 GLN cc_start: 0.7628 (mp10) cc_final: 0.7227 (mp10) REVERT: C 629 MET cc_start: 0.7204 (mmm) cc_final: 0.6210 (tmm) REVERT: E 9 MET cc_start: 0.5415 (tpt) cc_final: 0.4982 (tpp) REVERT: F 31 TYR cc_start: 0.7875 (m-80) cc_final: 0.7628 (m-10) REVERT: F 188 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8817 (mp) REVERT: G 9 MET cc_start: 0.5592 (tpt) cc_final: 0.5330 (tpp) REVERT: H 31 TYR cc_start: 0.7740 (m-80) cc_final: 0.7410 (m-10) REVERT: H 188 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8779 (mp) outliers start: 56 outliers final: 37 residues processed: 328 average time/residue: 0.3156 time to fit residues: 153.1039 Evaluate side-chains 285 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 2.192 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 792 VAL 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 760 ASP Chi-restraints excluded: chain C residue 792 VAL 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 625 THR Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 39 CYS 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 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 116 MET Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 194 VAL 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 39 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 HIS F 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.168490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133261 restraints weight = 27415.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134550 restraints weight = 39553.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136216 restraints weight = 33436.760| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18702 Z= 0.208 Angle : 0.630 11.212 25234 Z= 0.332 Chirality : 0.044 0.176 2826 Planarity : 0.004 0.048 3106 Dihedral : 4.455 42.136 2526 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 4.14 % Allowed : 13.35 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2298 helix: 1.71 (0.15), residues: 1232 sheet: -0.59 (0.40), residues: 148 loop : -1.13 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 578 HIS 0.006 0.001 HIS F 198 PHE 0.018 0.002 PHE A 495 TYR 0.017 0.002 TYR A 533 ARG 0.005 0.001 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.06997 ( 947) hydrogen bonds : angle 4.25541 ( 2709) SS BOND : bond 0.00375 ( 12) SS BOND : angle 1.42516 ( 24) covalent geometry : bond 0.00501 (18690) covalent geometry : angle 0.62914 (25210) *********************** 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 338 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 257 time to evaluate : 2.120 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: 0.7489 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: B 721 MET cc_start: 0.7912 (ppp) cc_final: 0.7648 (ppp) REVERT: B 756 GLN cc_start: 0.7750 (mp10) cc_final: 0.7319 (mp10) REVERT: D 587 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: D 756 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: F 31 TYR cc_start: 0.7962 (m-80) cc_final: 0.7646 (m-10) REVERT: F 188 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8869 (mp) REVERT: H 31 TYR cc_start: 0.7947 (m-80) cc_final: 0.7672 (m-10) REVERT: H 188 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8844 (mp) outliers start: 81 outliers final: 57 residues processed: 319 average time/residue: 0.3046 time to fit residues: 145.8263 Evaluate side-chains 292 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 2.166 ------------------------------------------------------------------------------- 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 400 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain B residue 395 VAL 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 617 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 395 VAL 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 587 GLN Chi-restraints excluded: chain D residue 615 SER 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 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 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 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 68 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 199 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 119 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 168 optimal weight: 0.0470 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN C 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.169899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135127 restraints weight = 27554.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139040 restraints weight = 40821.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.139259 restraints weight = 28014.851| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4386 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= 0.154 Angle : 0.558 8.574 25234 Z= 0.293 Chirality : 0.041 0.164 2826 Planarity : 0.004 0.045 3106 Dihedral : 4.177 35.554 2526 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.44 % Favored : 97.48 % Rotamer: Outliers : 4.04 % Allowed : 15.35 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 2298 helix: 1.91 (0.15), residues: 1234 sheet: -0.49 (0.42), residues: 146 loop : -1.08 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 578 HIS 0.004 0.001 HIS F 198 PHE 0.015 0.002 PHE F 72 TYR 0.013 0.001 TYR A 533 ARG 0.012 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.05796 ( 947) hydrogen bonds : angle 3.99795 ( 2709) SS BOND : bond 0.00244 ( 12) SS BOND : angle 1.20021 ( 24) covalent geometry : bond 0.00362 (18690) covalent geometry : angle 0.55704 (25210) *********************** 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 322 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 243 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLN cc_start: 0.5503 (pp30) cc_final: 0.5203 (tt0) REVERT: A 816 TYR cc_start: 0.7016 (t80) cc_final: 0.6781 (t80) REVERT: B 756 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: D 587 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: D 756 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: F 31 TYR cc_start: 0.7880 (m-80) cc_final: 0.7551 (m-10) REVERT: F 188 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8806 (mp) REVERT: G 9 MET cc_start: 0.5777 (tpt) cc_final: 0.5429 (tpp) REVERT: H 31 TYR cc_start: 0.7907 (m-80) cc_final: 0.7583 (m-10) REVERT: H 64 ARG cc_start: 0.7129 (ptp-170) cc_final: 0.6580 (ptp-110) REVERT: H 188 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8767 (mp) outliers start: 79 outliers final: 52 residues processed: 302 average time/residue: 0.2983 time to fit residues: 135.9076 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 : 2.044 ------------------------------------------------------------------------------- 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 463 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 714 GLN 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 508 GLN Chi-restraints excluded: chain B residue 614 SER 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 398 THR Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 414 MET 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 C residue 795 VAL Chi-restraints excluded: chain D residue 395 VAL 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 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 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 25 ILE Chi-restraints excluded: chain F residue 55 GLU 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 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 186 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 212 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN E 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.172785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138061 restraints weight = 27642.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.140144 restraints weight = 40121.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141153 restraints weight = 34646.330| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18702 Z= 0.119 Angle : 0.530 9.662 25234 Z= 0.276 Chirality : 0.040 0.163 2826 Planarity : 0.004 0.042 3106 Dihedral : 3.942 33.374 2526 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.35 % Rotamer: Outliers : 3.22 % Allowed : 16.01 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2298 helix: 2.17 (0.15), residues: 1234 sheet: -0.56 (0.40), residues: 170 loop : -0.92 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 177 HIS 0.003 0.001 HIS F 59 PHE 0.010 0.001 PHE B 546 TYR 0.013 0.001 TYR A 647 ARG 0.014 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 947) hydrogen bonds : angle 3.76327 ( 2709) SS BOND : bond 0.00193 ( 12) SS BOND : angle 1.00102 ( 24) covalent geometry : bond 0.00266 (18690) covalent geometry : angle 0.52907 (25210) *********************** 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 308 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 245 time to evaluate : 2.074 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: symmetry clash REVERT: A 816 TYR cc_start: 0.7034 (t80) cc_final: 0.6731 (t80) REVERT: B 756 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: C 601 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7814 (t) REVERT: D 756 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: E 9 MET cc_start: 0.5253 (tpt) cc_final: 0.4794 (tpp) REVERT: E 98 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7385 (mpt180) REVERT: F 31 TYR cc_start: 0.7859 (m-80) cc_final: 0.7534 (m-10) REVERT: F 188 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8782 (mp) REVERT: G 9 MET cc_start: 0.5544 (tpt) cc_final: 0.5253 (tpp) REVERT: H 31 TYR cc_start: 0.7870 (m-80) cc_final: 0.7587 (m-10) REVERT: H 64 ARG cc_start: 0.7141 (ptp-170) cc_final: 0.6595 (ptp-110) REVERT: H 188 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8738 (mp) outliers start: 63 outliers final: 47 residues processed: 292 average time/residue: 0.3021 time to fit residues: 133.2515 Evaluate side-chains 287 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 463 MET Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 721 MET 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 614 SER 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 411 ASN Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 712 ILE 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 626 VAL 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 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 55 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 171 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 130 optimal weight: 0.0040 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 198 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 0.5130 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.157708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123427 restraints weight = 27162.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126738 restraints weight = 57084.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127665 restraints weight = 28754.442| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4712 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= 0.111 Angle : 0.518 9.605 25234 Z= 0.268 Chirality : 0.040 0.170 2826 Planarity : 0.004 0.038 3106 Dihedral : 3.774 32.923 2526 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Rotamer: Outliers : 2.81 % Allowed : 16.47 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.18), residues: 2298 helix: 2.29 (0.15), residues: 1238 sheet: -0.59 (0.39), residues: 160 loop : -1.09 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 605 HIS 0.003 0.000 HIS F 59 PHE 0.025 0.001 PHE H 72 TYR 0.015 0.001 TYR A 647 ARG 0.006 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 947) hydrogen bonds : angle 3.65316 ( 2709) SS BOND : bond 0.00163 ( 12) SS BOND : angle 0.87369 ( 24) covalent geometry : bond 0.00247 (18690) covalent geometry : angle 0.51786 (25210) *********************** 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: 55 poor density : 252 time to evaluate : 1.889 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: symmetry clash REVERT: A 647 TYR cc_start: 0.6249 (p90) cc_final: 0.5529 (p90) REVERT: A 714 GLN cc_start: 0.6850 (tm-30) cc_final: 0.5959 (tm-30) REVERT: A 816 TYR cc_start: 0.6933 (t80) cc_final: 0.6629 (t80) REVERT: B 756 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: D 638 ASP cc_start: 0.8169 (m-30) cc_final: 0.7825 (t0) REVERT: D 756 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7517 (mp10) REVERT: E 9 MET cc_start: 0.5195 (tpt) cc_final: 0.4712 (tpp) REVERT: E 98 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7438 (mpt180) REVERT: F 31 TYR cc_start: 0.7914 (m-80) cc_final: 0.7596 (m-10) REVERT: F 188 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8778 (mp) REVERT: G 9 MET cc_start: 0.5521 (tpt) cc_final: 0.5240 (tpp) REVERT: H 31 TYR cc_start: 0.7922 (m-80) cc_final: 0.7633 (m-10) REVERT: H 65 THR cc_start: 0.6993 (t) cc_final: 0.6705 (t) REVERT: H 188 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8722 (mp) outliers start: 55 outliers final: 41 residues processed: 297 average time/residue: 0.3133 time to fit residues: 138.3172 Evaluate side-chains 282 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 1.925 ------------------------------------------------------------------------------- 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 463 MET 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 615 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 795 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 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 E residue 21 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 68 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 128 optimal weight: 2.9990 chunk 12 optimal weight: 0.0050 chunk 129 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 230 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.168877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134736 restraints weight = 27392.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137665 restraints weight = 43204.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138318 restraints weight = 31935.924| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4911 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= 0.172 Angle : 0.594 10.038 25234 Z= 0.309 Chirality : 0.042 0.188 2826 Planarity : 0.004 0.043 3106 Dihedral : 4.055 39.901 2526 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 3.68 % Allowed : 16.47 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2298 helix: 2.09 (0.15), residues: 1236 sheet: -0.61 (0.40), residues: 148 loop : -1.20 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 578 HIS 0.003 0.001 HIS F 198 PHE 0.016 0.002 PHE A 546 TYR 0.016 0.001 TYR A 533 ARG 0.009 0.001 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.06146 ( 947) hydrogen bonds : angle 3.93621 ( 2709) SS BOND : bond 0.00256 ( 12) SS BOND : angle 1.04179 ( 24) covalent geometry : bond 0.00410 (18690) covalent geometry : angle 0.59366 (25210) *********************** 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 311 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 239 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8011 (t) REVERT: B 756 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: C 601 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8052 (t) REVERT: C 816 TYR cc_start: 0.6965 (t80) cc_final: 0.6705 (t80) REVERT: D 638 ASP cc_start: 0.8119 (m-30) cc_final: 0.7915 (t0) REVERT: D 756 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: F 31 TYR cc_start: 0.7950 (m-80) cc_final: 0.7723 (m-10) REVERT: F 188 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8816 (mp) REVERT: G 9 MET cc_start: 0.5815 (tpt) cc_final: 0.5469 (tpp) REVERT: G 39 CYS cc_start: 0.3854 (OUTLIER) cc_final: 0.3385 (m) REVERT: H 31 TYR cc_start: 0.7927 (m-80) cc_final: 0.7656 (m-10) REVERT: H 188 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8778 (mp) outliers start: 72 outliers final: 57 residues processed: 295 average time/residue: 0.3064 time to fit residues: 138.6276 Evaluate side-chains 296 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 463 MET 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 A residue 714 GLN 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 614 SER 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 B residue 788 SER 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 601 VAL Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 795 VAL 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 788 SER Chi-restraints excluded: chain E residue 21 SER 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 194 VAL 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 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 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 127 TYR 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 184 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 226 optimal weight: 0.0980 chunk 41 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.172155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138351 restraints weight = 27832.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137408 restraints weight = 35634.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.138841 restraints weight = 34614.208| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18702 Z= 0.122 Angle : 0.544 10.077 25234 Z= 0.281 Chirality : 0.040 0.173 2826 Planarity : 0.004 0.039 3106 Dihedral : 3.838 34.231 2526 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 2.97 % Allowed : 17.03 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2298 helix: 2.26 (0.15), residues: 1236 sheet: -0.54 (0.41), residues: 148 loop : -1.19 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 177 HIS 0.003 0.001 HIS H 59 PHE 0.018 0.001 PHE H 72 TYR 0.018 0.001 TYR C 673 ARG 0.008 0.001 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 947) hydrogen bonds : angle 3.69124 ( 2709) SS BOND : bond 0.00154 ( 12) SS BOND : angle 0.86771 ( 24) covalent geometry : bond 0.00277 (18690) covalent geometry : angle 0.54409 (25210) *********************** 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 293 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 647 TYR cc_start: 0.6353 (p90) cc_final: 0.5758 (p90) REVERT: B 756 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: C 601 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7785 (t) REVERT: C 674 MET cc_start: 0.7448 (mmm) cc_final: 0.7177 (mmm) REVERT: C 816 TYR cc_start: 0.6989 (t80) cc_final: 0.6689 (t80) REVERT: D 638 ASP cc_start: 0.8102 (m-30) cc_final: 0.7812 (t0) REVERT: D 756 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: E 9 MET cc_start: 0.5194 (tpt) cc_final: 0.4705 (tpp) REVERT: E 39 CYS cc_start: 0.3984 (OUTLIER) cc_final: 0.3516 (m) REVERT: F 31 TYR cc_start: 0.7903 (m-80) cc_final: 0.7594 (m-10) REVERT: F 188 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8786 (mp) REVERT: G 9 MET cc_start: 0.5592 (tpt) cc_final: 0.5271 (tpp) REVERT: G 39 CYS cc_start: 0.3549 (OUTLIER) cc_final: 0.3312 (m) REVERT: H 31 TYR cc_start: 0.7855 (m-80) cc_final: 0.7587 (m-10) REVERT: H 188 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8749 (mp) outliers start: 58 outliers final: 47 residues processed: 282 average time/residue: 0.2876 time to fit residues: 122.9165 Evaluate side-chains 284 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 463 MET Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 714 GLN 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 614 SER 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 B residue 788 SER 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 601 VAL Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 795 VAL 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 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 116 MET Chi-restraints excluded: chain E residue 194 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 46 optimal weight: 0.0000 chunk 127 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN F 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123008 restraints weight = 27177.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125644 restraints weight = 51652.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127027 restraints weight = 32482.419| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18702 Z= 0.107 Angle : 0.539 10.246 25234 Z= 0.277 Chirality : 0.039 0.169 2826 Planarity : 0.004 0.037 3106 Dihedral : 3.720 31.833 2526 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 2.56 % Allowed : 17.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2298 helix: 2.43 (0.15), residues: 1234 sheet: -0.50 (0.42), residues: 146 loop : -1.15 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 671 HIS 0.004 0.000 HIS E 59 PHE 0.015 0.001 PHE H 72 TYR 0.016 0.001 TYR C 673 ARG 0.008 0.001 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 947) hydrogen bonds : angle 3.54107 ( 2709) SS BOND : bond 0.00146 ( 12) SS BOND : angle 1.10695 ( 24) covalent geometry : bond 0.00231 (18690) covalent geometry : angle 0.53772 (25210) ********************** 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 296 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7636 (t) REVERT: A 647 TYR cc_start: 0.5912 (p90) cc_final: 0.5255 (p90) REVERT: B 756 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: C 601 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7629 (t) REVERT: C 674 MET cc_start: 0.7440 (mmm) cc_final: 0.7144 (mmm) REVERT: C 816 TYR cc_start: 0.6946 (t80) cc_final: 0.6599 (t80) REVERT: D 638 ASP cc_start: 0.8145 (m-30) cc_final: 0.7688 (t0) REVERT: D 756 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: E 39 CYS cc_start: 0.3673 (OUTLIER) cc_final: 0.3346 (m) REVERT: E 98 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7424 (mpt180) REVERT: F 188 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8770 (mp) REVERT: G 9 MET cc_start: 0.5452 (tpt) cc_final: 0.5176 (tpp) REVERT: H 31 TYR cc_start: 0.7884 (m-80) cc_final: 0.7541 (m-10) REVERT: H 188 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8743 (mp) outliers start: 50 outliers final: 38 residues processed: 286 average time/residue: 0.3046 time to fit residues: 130.7639 Evaluate side-chains 278 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 463 MET 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 488 VAL 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 756 GLN Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain D residue 488 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 E residue 21 SER Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 194 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 225 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 619 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120892 restraints weight = 27435.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123637 restraints weight = 61318.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125445 restraints weight = 30060.661| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18702 Z= 0.151 Angle : 0.584 10.868 25234 Z= 0.303 Chirality : 0.041 0.195 2826 Planarity : 0.004 0.068 3106 Dihedral : 3.881 38.423 2526 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 2.81 % Allowed : 17.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2298 helix: 2.22 (0.15), residues: 1246 sheet: -0.57 (0.41), residues: 148 loop : -1.20 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 671 HIS 0.003 0.001 HIS F 59 PHE 0.017 0.001 PHE H 72 TYR 0.015 0.001 TYR F 31 ARG 0.008 0.001 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.05515 ( 947) hydrogen bonds : angle 3.78973 ( 2709) SS BOND : bond 0.00272 ( 12) SS BOND : angle 1.13481 ( 24) covalent geometry : bond 0.00357 (18690) covalent geometry : angle 0.58334 (25210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5381.63 seconds wall clock time: 95 minutes 16.42 seconds (5716.42 seconds total)