Starting phenix.real_space_refine on Mon May 19 10:08:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dht_46876/05_2025/9dht_46876.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dht_46876/05_2025/9dht_46876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dht_46876/05_2025/9dht_46876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dht_46876/05_2025/9dht_46876.map" model { file = "/net/cci-nas-00/data/ceres_data/9dht_46876/05_2025/9dht_46876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dht_46876/05_2025/9dht_46876.cif" } resolution = 4.31 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= 0.011 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 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18294 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': 2, 'PTRANS': 11, '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': 1, 'PTRANS': 12, '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': 2, 'PTRANS': 11, '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': 1, 'PTRANS': 12, '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: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} 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: 12.38, per 1000 atoms: 0.68 Number of scatterers: 18294 At special positions: 0 Unit cell: (112.52, 133.86, 152.29, 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 3314 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: 4.72 Conformation dependent library (CDL) restraints added in 2.3 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: 100 helices and 21 sheets defined 58.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 4.168A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.662A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.870A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.650A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.682A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.629A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 removed outlier: 4.549A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 3.646A 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 818 removed outlier: 4.352A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.963A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 522 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 523 through 546 removed outlier: 4.273A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.501A pdb=" N PHE B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.791A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.702A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.507A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.676A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.787A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 3.544A pdb=" N LEU B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.534A pdb=" N LYS B 776 " --> pdb=" O CYS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 817 removed outlier: 4.420A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 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 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 521 through 545 removed outlier: 4.249A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 4.284A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C 582 " --> pdb=" O TRP C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 removed outlier: 3.609A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET C 629 " --> pdb=" O THR C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.924A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.733A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 786 removed outlier: 4.134A pdb=" N SER C 785 " --> pdb=" O GLU C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 792 Processing helix chain 'C' and resid 793 through 818 removed outlier: 4.072A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.670A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 removed outlier: 3.935A pdb=" N LEU D 428 " --> pdb=" O TYR D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 520 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 521 through 545 removed outlier: 4.430A pdb=" N ILE D 525 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 586 Processing helix chain 'D' and resid 595 through 624 removed outlier: 3.754A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.750A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.618A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.846A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 749 " --> pdb=" O PRO D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 removed outlier: 4.260A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 817 removed outlier: 4.206A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.712A pdb=" N LEU E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA E 16 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE E 17 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.776A pdb=" N PHE E 96 " --> pdb=" O ALA E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 104 removed outlier: 3.688A pdb=" N ARG E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 124 removed outlier: 4.019A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 160 removed outlier: 4.219A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 206 removed outlier: 4.008A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 28 Processing helix chain 'F' and resid 94 through 104 removed outlier: 4.558A pdb=" N ALA F 99 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL F 100 " --> pdb=" O PHE F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.560A pdb=" N ILE F 108 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS F 120 " --> pdb=" O MET F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 131 through 159 removed outlier: 3.745A pdb=" N ALA F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 206 removed outlier: 3.993A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'G' and resid 7 through 28 Processing helix chain 'G' and resid 94 through 104 removed outlier: 4.765A pdb=" N ALA G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 123 removed outlier: 3.569A 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 131 through 161 removed outlier: 3.891A pdb=" N LEU G 135 " --> pdb=" O HIS G 131 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE G 149 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY G 161 " --> pdb=" O SER G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 206 removed outlier: 4.006A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 195 " --> pdb=" O MET G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'H' and resid 7 through 28 removed outlier: 3.664A pdb=" N LEU H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY H 15 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA H 16 " --> pdb=" O THR H 12 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE H 17 " --> pdb=" O THR H 13 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA H 18 " --> pdb=" O VAL H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 removed outlier: 3.821A pdb=" N PHE H 96 " --> pdb=" O ALA H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 93 through 96' Processing helix chain 'H' and resid 97 through 104 removed outlier: 3.697A pdb=" N ARG H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.969A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 160 removed outlier: 4.113A pdb=" N LEU H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 206 removed outlier: 4.039A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 205 " --> pdb=" O ILE H 201 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.378A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.897A 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 496 through 498 removed outlier: 4.131A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 682 through 683 removed outlier: 8.836A pdb=" N VAL A 683 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A 650 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N GLU A 705 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.803A 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 498 removed outlier: 5.211A pdb=" N ILE B 734 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR B 732 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET B 496 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS B 730 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.679A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 440 through 444 removed outlier: 5.870A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.982A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.674A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 439 through 444 removed outlier: 6.944A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 489 through 498 removed outlier: 7.469A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.586A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 78 removed outlier: 3.611A pdb=" N HIS E 59 " --> pdb=" O CYS E 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.535A pdb=" N SER F 174 " --> pdb=" O TYR F 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.641A pdb=" N SER G 174 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 76 through 78 removed outlier: 3.519A pdb=" N HIS H 59 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 174 " --> pdb=" O TYR H 34 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2724 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: 6.05 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5601 1.34 - 1.46: 4322 1.46 - 1.58: 8555 1.58 - 1.70: 0 1.70 - 1.81: 208 Bond restraints: 18686 Sorted by residual: bond pdb=" N GLN A 587 " pdb=" CA GLN A 587 " ideal model delta sigma weight residual 1.458 1.487 -0.028 1.08e-02 8.57e+03 6.90e+00 bond pdb=" N MET A 629 " pdb=" CA MET A 629 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.44e-02 4.82e+03 6.73e+00 bond pdb=" CG1 ILE F 188 " pdb=" CD1 ILE F 188 " ideal model delta sigma weight residual 1.513 1.412 0.101 3.90e-02 6.57e+02 6.68e+00 bond pdb=" N GLN B 586 " pdb=" CA GLN B 586 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.65e+00 bond pdb=" N GLN A 586 " pdb=" CA GLN A 586 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.45e-02 4.76e+03 5.71e+00 ... (remaining 18681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 24473 1.74 - 3.47: 632 3.47 - 5.21: 84 5.21 - 6.95: 11 6.95 - 8.69: 2 Bond angle restraints: 25202 Sorted by residual: angle pdb=" C MET B 629 " pdb=" N VAL B 630 " pdb=" CA VAL B 630 " ideal model delta sigma weight residual 121.97 130.66 -8.69 1.80e+00 3.09e-01 2.33e+01 angle pdb=" C GLU B 402 " pdb=" N SER B 403 " pdb=" CA SER B 403 " ideal model delta sigma weight residual 120.06 124.79 -4.73 1.19e+00 7.06e-01 1.58e+01 angle pdb=" CA MET B 585 " pdb=" C MET B 585 " pdb=" O MET B 585 " ideal model delta sigma weight residual 121.02 117.37 3.65 1.15e+00 7.56e-01 1.01e+01 angle pdb=" C GLY B 725 " pdb=" N ASN B 726 " pdb=" CA ASN B 726 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" CA PHE A 584 " pdb=" C PHE A 584 " pdb=" O PHE A 584 " ideal model delta sigma weight residual 120.82 117.51 3.31 1.05e+00 9.07e-01 9.92e+00 ... (remaining 25197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10253 17.95 - 35.89: 603 35.89 - 53.84: 83 53.84 - 71.78: 26 71.78 - 89.73: 11 Dihedral angle restraints: 10976 sinusoidal: 4270 harmonic: 6706 Sorted by residual: dihedral pdb=" CA VAL E 14 " pdb=" C VAL E 14 " pdb=" N GLY E 15 " pdb=" CA GLY E 15 " ideal model delta harmonic sigma weight residual 180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA SER G 60 " pdb=" C SER G 60 " pdb=" N GLY G 61 " pdb=" CA GLY G 61 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA VAL H 14 " pdb=" C VAL H 14 " pdb=" N GLY H 15 " pdb=" CA GLY H 15 " ideal model delta harmonic sigma weight residual -180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 10973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1940 0.042 - 0.084: 681 0.084 - 0.126: 176 0.126 - 0.167: 25 0.167 - 0.209: 4 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA THR B 744 " pdb=" N THR B 744 " pdb=" C THR B 744 " pdb=" CB THR B 744 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.03e+00 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 2.33 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2823 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 582 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C GLY B 582 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY B 582 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 583 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 520 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 545 " -0.163 9.50e-02 1.11e+02 7.37e-02 4.37e+00 pdb=" NE ARG C 545 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 545 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 545 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 545 " 0.000 2.00e-02 2.50e+03 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 422 2.70 - 3.25: 19962 3.25 - 3.80: 27882 3.80 - 4.35: 34556 4.35 - 4.90: 57217 Nonbonded interactions: 140039 Sorted by model distance: nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.147 3.040 nonbonded pdb=" O PRO A 478 " pdb=" N GLU A1301 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU B 657 " pdb=" NH1 ARG B 660 " model vdw 2.254 3.120 nonbonded pdb=" N GLU G 94 " pdb=" OE1 GLU G 94 " model vdw 2.263 3.120 nonbonded pdb=" OG SER D 547 " pdb=" OE2 GLU D 566 " model vdw 2.279 3.040 ... (remaining 140034 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: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.230 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 0.101 18698 Z= 0.158 Angle : 0.665 8.686 25226 Z= 0.383 Chirality : 0.045 0.209 2826 Planarity : 0.006 0.074 3102 Dihedral : 12.373 89.727 6664 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.35 % Favored : 94.30 % Rotamer: Outliers : 0.31 % Allowed : 0.05 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.97 (0.16), residues: 2298 helix: -0.05 (0.14), residues: 1179 sheet: -1.18 (0.42), residues: 144 loop : -1.20 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 63 HIS 0.003 0.001 HIS H 131 PHE 0.020 0.002 PHE E 179 TYR 0.018 0.003 TYR C 732 ARG 0.018 0.002 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.16050 ( 952) hydrogen bonds : angle 6.13905 ( 2724) SS BOND : bond 0.00165 ( 12) SS BOND : angle 0.57251 ( 24) covalent geometry : bond 0.00311 (18686) covalent geometry : angle 0.66492 (25202) *********************** 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 630 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 624 time to evaluate : 2.045 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 450 TYR cc_start: 0.6301 (m-80) cc_final: 0.5605 (m-80) REVERT: A 529 ILE cc_start: 0.9309 (mt) cc_final: 0.9094 (mt) REVERT: A 569 ASN cc_start: 0.7755 (p0) cc_final: 0.6161 (m-40) REVERT: A 575 ASN cc_start: 0.8218 (m-40) cc_final: 0.7981 (t0) REVERT: A 576 SER cc_start: 0.9309 (m) cc_final: 0.9071 (p) REVERT: A 670 MET cc_start: 0.8992 (mtt) cc_final: 0.8664 (mtt) REVERT: B 435 HIS cc_start: 0.5843 (m-70) cc_final: 0.5169 (m-70) REVERT: B 573 ILE cc_start: 0.9124 (tp) cc_final: 0.8862 (tt) REVERT: B 590 ASP cc_start: 0.7229 (p0) cc_final: 0.6910 (p0) REVERT: B 708 MET cc_start: 0.7845 (mpp) cc_final: 0.7429 (mpp) REVERT: C 491 PHE cc_start: 0.6683 (m-80) cc_final: 0.6407 (m-80) REVERT: C 527 MET cc_start: 0.7848 (ttp) cc_final: 0.7625 (ttp) REVERT: C 538 VAL cc_start: 0.9518 (t) cc_final: 0.9214 (p) REVERT: C 585 MET cc_start: 0.8720 (mmt) cc_final: 0.8262 (mmt) REVERT: C 600 ILE cc_start: 0.8964 (mt) cc_final: 0.8717 (mm) REVERT: C 650 LEU cc_start: 0.8343 (tp) cc_final: 0.7817 (tp) REVERT: C 670 MET cc_start: 0.9024 (mtt) cc_final: 0.7998 (mmt) REVERT: C 811 LEU cc_start: 0.8848 (mm) cc_final: 0.8555 (tp) REVERT: D 543 VAL cc_start: 0.9336 (m) cc_final: 0.9047 (t) REVERT: D 767 TRP cc_start: 0.6326 (m-90) cc_final: 0.6105 (m-90) REVERT: E 156 ILE cc_start: 0.8797 (mm) cc_final: 0.8569 (mt) REVERT: E 159 ASN cc_start: 0.8357 (m-40) cc_final: 0.8126 (t0) REVERT: F 111 VAL cc_start: 0.9408 (t) cc_final: 0.9172 (t) REVERT: F 188 ILE cc_start: 0.8558 (mp) cc_final: 0.7993 (mp) REVERT: F 197 VAL cc_start: 0.9263 (t) cc_final: 0.9041 (p) REVERT: G 130 ARG cc_start: 0.5290 (mtt180) cc_final: 0.4975 (ttt90) REVERT: G 142 VAL cc_start: 0.8574 (t) cc_final: 0.8326 (t) REVERT: H 30 ASP cc_start: 0.6565 (m-30) cc_final: 0.6130 (m-30) outliers start: 6 outliers final: 1 residues processed: 624 average time/residue: 0.3097 time to fit residues: 282.7300 Evaluate side-chains 328 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 2.300 ------------------------------------------------------------------------------- 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: 0.9980 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 0.0030 chunk 210 optimal weight: 0.7980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 642 GLN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN H 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.140610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.105516 restraints weight = 49188.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104481 restraints weight = 67949.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105100 restraints weight = 60076.715| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18698 Z= 0.176 Angle : 0.655 7.624 25226 Z= 0.357 Chirality : 0.044 0.242 2826 Planarity : 0.004 0.053 3102 Dihedral : 5.686 62.220 2522 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.35 % Favored : 96.39 % Rotamer: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.64 (0.18), residues: 2298 helix: 1.52 (0.15), residues: 1190 sheet: -1.10 (0.41), residues: 154 loop : -0.69 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 177 HIS 0.003 0.001 HIS A 412 PHE 0.040 0.002 PHE G 140 TYR 0.017 0.002 TYR E 175 ARG 0.004 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.05751 ( 952) hydrogen bonds : angle 4.92385 ( 2724) SS BOND : bond 0.00590 ( 12) SS BOND : angle 2.76878 ( 24) covalent geometry : bond 0.00392 (18686) covalent geometry : angle 0.64989 (25202) *********************** 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 394 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 392 time to evaluate : 2.091 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.6654 (m-80) cc_final: 0.5877 (m-10) REVERT: A 496 MET cc_start: 0.5166 (ttp) cc_final: 0.4950 (ttp) REVERT: A 576 SER cc_start: 0.9528 (m) cc_final: 0.9307 (p) REVERT: A 708 MET cc_start: 0.8167 (mtt) cc_final: 0.7571 (mtt) REVERT: B 503 MET cc_start: 0.7829 (ttm) cc_final: 0.7424 (ttm) REVERT: B 544 SER cc_start: 0.9258 (m) cc_final: 0.8954 (p) REVERT: B 573 ILE cc_start: 0.9380 (tp) cc_final: 0.8862 (tt) REVERT: B 577 LEU cc_start: 0.9314 (mt) cc_final: 0.9114 (mt) REVERT: B 702 TYR cc_start: 0.7005 (t80) cc_final: 0.6726 (t80) REVERT: B 708 MET cc_start: 0.8094 (mpp) cc_final: 0.7816 (mpp) REVERT: C 491 PHE cc_start: 0.6990 (m-80) cc_final: 0.6784 (m-10) REVERT: C 576 SER cc_start: 0.9657 (m) cc_final: 0.9448 (p) REVERT: C 650 LEU cc_start: 0.8367 (tp) cc_final: 0.7734 (tp) REVERT: C 670 MET cc_start: 0.9177 (mtt) cc_final: 0.8600 (mtt) REVERT: C 708 MET cc_start: 0.8253 (mtt) cc_final: 0.8029 (mtt) REVERT: C 811 LEU cc_start: 0.8890 (mm) cc_final: 0.8628 (tp) REVERT: D 585 MET cc_start: 0.9071 (mmt) cc_final: 0.8853 (mmt) REVERT: E 81 HIS cc_start: 0.7754 (m90) cc_final: 0.7531 (m-70) REVERT: E 181 PHE cc_start: 0.7711 (m-80) cc_final: 0.7451 (m-80) REVERT: E 199 MET cc_start: 0.8367 (tpt) cc_final: 0.8075 (tpp) REVERT: F 130 ARG cc_start: 0.4919 (mtt180) cc_final: 0.3886 (ttt180) REVERT: F 187 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8236 (mm) REVERT: F 188 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8539 (mp) REVERT: F 197 VAL cc_start: 0.9529 (t) cc_final: 0.9286 (p) REVERT: G 130 ARG cc_start: 0.5295 (mtt180) cc_final: 0.4641 (ttt90) REVERT: H 57 MET cc_start: 0.7645 (mpp) cc_final: 0.7445 (mpp) REVERT: H 199 MET cc_start: 0.8590 (tpp) cc_final: 0.8087 (tpp) outliers start: 2 outliers final: 0 residues processed: 394 average time/residue: 0.2896 time to fit residues: 173.8424 Evaluate side-chains 288 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 223 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS C 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN G 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.141522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.106081 restraints weight = 48690.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.102878 restraints weight = 39136.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103474 restraints weight = 38194.651| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18698 Z= 0.134 Angle : 0.582 7.099 25226 Z= 0.314 Chirality : 0.042 0.172 2826 Planarity : 0.004 0.041 3102 Dihedral : 5.157 64.723 2522 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.35 % Favored : 96.43 % Rotamer: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.98 (0.18), residues: 2298 helix: 1.87 (0.15), residues: 1206 sheet: -0.94 (0.42), residues: 152 loop : -0.68 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 177 HIS 0.004 0.001 HIS F 131 PHE 0.025 0.001 PHE H 96 TYR 0.023 0.001 TYR B 450 ARG 0.003 0.000 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 952) hydrogen bonds : angle 4.46227 ( 2724) SS BOND : bond 0.00806 ( 12) SS BOND : angle 1.45063 ( 24) covalent geometry : bond 0.00274 (18686) covalent geometry : angle 0.58084 (25202) *********************** 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 385 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 381 time to evaluate : 1.916 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.6751 (m-80) cc_final: 0.5969 (m-80) REVERT: A 573 ILE cc_start: 0.9137 (tp) cc_final: 0.8915 (tp) REVERT: A 576 SER cc_start: 0.9556 (m) cc_final: 0.9242 (p) REVERT: A 587 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7996 (mp10) REVERT: A 650 LEU cc_start: 0.8489 (tp) cc_final: 0.8257 (tp) REVERT: A 670 MET cc_start: 0.8938 (mtm) cc_final: 0.8213 (mtm) REVERT: A 674 MET cc_start: 0.7642 (mmm) cc_final: 0.7391 (mmm) REVERT: A 708 MET cc_start: 0.8419 (mtt) cc_final: 0.8176 (mtt) REVERT: A 710 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8848 (pm20) REVERT: B 503 MET cc_start: 0.7619 (ttm) cc_final: 0.7344 (ttm) REVERT: B 544 SER cc_start: 0.9156 (m) cc_final: 0.8853 (p) REVERT: B 573 ILE cc_start: 0.9313 (tp) cc_final: 0.8911 (tt) REVERT: B 702 TYR cc_start: 0.6800 (t80) cc_final: 0.6599 (t80) REVERT: B 812 ILE cc_start: 0.8118 (tt) cc_final: 0.7876 (tt) REVERT: C 576 SER cc_start: 0.9652 (m) cc_final: 0.9395 (p) REVERT: C 650 LEU cc_start: 0.8288 (tp) cc_final: 0.7776 (tp) REVERT: C 670 MET cc_start: 0.9139 (mtt) cc_final: 0.8009 (mmp) REVERT: C 708 MET cc_start: 0.8435 (mtt) cc_final: 0.8229 (mtt) REVERT: C 811 LEU cc_start: 0.8909 (mm) cc_final: 0.8661 (tp) REVERT: D 503 MET cc_start: 0.7416 (ttm) cc_final: 0.7211 (ttm) REVERT: D 702 TYR cc_start: 0.7233 (t80) cc_final: 0.7007 (t80) REVERT: D 714 GLN cc_start: 0.8551 (mp10) cc_final: 0.8035 (pm20) REVERT: D 788 SER cc_start: 0.8907 (p) cc_final: 0.8499 (m) REVERT: E 81 HIS cc_start: 0.7715 (m90) cc_final: 0.7507 (m-70) REVERT: E 199 MET cc_start: 0.8346 (tpt) cc_final: 0.8073 (tpp) REVERT: F 32 TRP cc_start: 0.8199 (m100) cc_final: 0.7961 (m100) REVERT: F 130 ARG cc_start: 0.4823 (mtt180) cc_final: 0.3711 (ttt180) REVERT: F 187 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8101 (mt) REVERT: F 188 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8630 (mp) REVERT: F 197 VAL cc_start: 0.9511 (t) cc_final: 0.9298 (p) REVERT: G 32 TRP cc_start: 0.8157 (m100) cc_final: 0.7906 (m100) REVERT: G 119 LEU cc_start: 0.8694 (pp) cc_final: 0.8395 (mp) REVERT: G 130 ARG cc_start: 0.5483 (mtt180) cc_final: 0.4595 (ttt180) REVERT: G 134 ILE cc_start: 0.7784 (mm) cc_final: 0.7407 (mm) REVERT: H 57 MET cc_start: 0.7649 (mpp) cc_final: 0.7374 (mpp) REVERT: H 199 MET cc_start: 0.8601 (tpp) cc_final: 0.8154 (tpp) outliers start: 4 outliers final: 0 residues processed: 385 average time/residue: 0.2897 time to fit residues: 169.7159 Evaluate side-chains 297 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 294 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 147 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 227 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN B 714 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.105453 restraints weight = 50146.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.101711 restraints weight = 61148.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102721 restraints weight = 58404.215| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18698 Z= 0.150 Angle : 0.594 7.907 25226 Z= 0.319 Chirality : 0.042 0.172 2826 Planarity : 0.004 0.041 3102 Dihedral : 4.958 65.155 2522 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 1.01 (0.18), residues: 2298 helix: 1.85 (0.15), residues: 1212 sheet: -0.90 (0.42), residues: 151 loop : -0.61 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 177 HIS 0.012 0.001 HIS B 435 PHE 0.023 0.002 PHE G 140 TYR 0.024 0.001 TYR C 647 ARG 0.006 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.04915 ( 952) hydrogen bonds : angle 4.45661 ( 2724) SS BOND : bond 0.00281 ( 12) SS BOND : angle 1.48986 ( 24) covalent geometry : bond 0.00328 (18686) covalent geometry : angle 0.59217 (25202) *********************** 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 342 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 2.058 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7035 (m-80) cc_final: 0.6426 (m-80) REVERT: A 576 SER cc_start: 0.9601 (m) cc_final: 0.9257 (p) REVERT: A 585 MET cc_start: 0.8917 (tpp) cc_final: 0.8591 (tpp) REVERT: A 650 LEU cc_start: 0.8386 (tp) cc_final: 0.8156 (tp) REVERT: A 670 MET cc_start: 0.8932 (mtm) cc_final: 0.7264 (tpp) REVERT: A 808 LEU cc_start: 0.9165 (pp) cc_final: 0.8930 (pp) REVERT: B 503 MET cc_start: 0.7724 (ttm) cc_final: 0.7513 (ttm) REVERT: B 544 SER cc_start: 0.9185 (m) cc_final: 0.8933 (p) REVERT: B 573 ILE cc_start: 0.9406 (tp) cc_final: 0.8927 (tt) REVERT: B 812 ILE cc_start: 0.8349 (tt) cc_final: 0.8110 (tt) REVERT: C 586 GLN cc_start: 0.8135 (mp10) cc_final: 0.7747 (mp10) REVERT: C 650 LEU cc_start: 0.8275 (tp) cc_final: 0.7797 (tp) REVERT: C 670 MET cc_start: 0.9155 (mtt) cc_final: 0.8800 (mtt) REVERT: C 811 LEU cc_start: 0.8826 (mm) cc_final: 0.8604 (tp) REVERT: D 503 MET cc_start: 0.7459 (ttm) cc_final: 0.7203 (ttm) REVERT: D 659 PHE cc_start: 0.8184 (m-80) cc_final: 0.7772 (m-80) REVERT: D 702 TYR cc_start: 0.7308 (t80) cc_final: 0.6922 (t80) REVERT: D 788 SER cc_start: 0.8710 (p) cc_final: 0.8269 (m) REVERT: E 57 MET cc_start: 0.7659 (mpp) cc_final: 0.7449 (mpp) REVERT: E 81 HIS cc_start: 0.7786 (m90) cc_final: 0.7560 (m-70) REVERT: E 199 MET cc_start: 0.8383 (tpt) cc_final: 0.8084 (tpp) REVERT: F 32 TRP cc_start: 0.8402 (m100) cc_final: 0.8109 (m100) REVERT: F 96 PHE cc_start: 0.6349 (t80) cc_final: 0.5950 (t80) REVERT: F 130 ARG cc_start: 0.5002 (mtt180) cc_final: 0.3867 (ttt180) REVERT: G 32 TRP cc_start: 0.8390 (m100) cc_final: 0.8066 (m100) REVERT: G 130 ARG cc_start: 0.5428 (mtt180) cc_final: 0.4305 (ttt180) REVERT: H 199 MET cc_start: 0.8525 (tpp) cc_final: 0.8055 (tpp) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2792 time to fit residues: 147.1389 Evaluate side-chains 267 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 82 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.134566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102649 restraints weight = 48887.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.098412 restraints weight = 61787.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099692 restraints weight = 53920.853| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18698 Z= 0.218 Angle : 0.674 10.118 25226 Z= 0.365 Chirality : 0.045 0.257 2826 Planarity : 0.004 0.050 3102 Dihedral : 5.214 72.922 2522 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.04 % Rotamer: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.53 (0.18), residues: 2298 helix: 1.45 (0.15), residues: 1216 sheet: -1.11 (0.42), residues: 152 loop : -0.84 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 177 HIS 0.015 0.002 HIS H 131 PHE 0.027 0.002 PHE G 140 TYR 0.022 0.002 TYR C 647 ARG 0.004 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.05999 ( 952) hydrogen bonds : angle 4.76949 ( 2724) SS BOND : bond 0.00324 ( 12) SS BOND : angle 1.34397 ( 24) covalent geometry : bond 0.00477 (18686) covalent geometry : angle 0.67345 (25202) *********************** 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 337 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 2.180 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.9028 (mtm) cc_final: 0.7950 (tpp) REVERT: A 710 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8790 (pm20) REVERT: A 727 LEU cc_start: 0.8407 (mp) cc_final: 0.7957 (tp) REVERT: A 808 LEU cc_start: 0.9254 (pp) cc_final: 0.8995 (pp) REVERT: B 812 ILE cc_start: 0.8478 (tt) cc_final: 0.8257 (tt) REVERT: C 670 MET cc_start: 0.9167 (mtt) cc_final: 0.8828 (mtt) REVERT: C 811 LEU cc_start: 0.9014 (mm) cc_final: 0.8543 (tp) REVERT: D 503 MET cc_start: 0.7533 (ttm) cc_final: 0.7315 (ttm) REVERT: D 519 ASP cc_start: 0.8242 (t70) cc_final: 0.8030 (t0) REVERT: D 585 MET cc_start: 0.9156 (mmt) cc_final: 0.8918 (tpp) REVERT: D 659 PHE cc_start: 0.8226 (m-80) cc_final: 0.7729 (m-80) REVERT: D 788 SER cc_start: 0.8712 (p) cc_final: 0.8328 (m) REVERT: D 817 LYS cc_start: 0.8098 (mttt) cc_final: 0.7737 (mmtp) REVERT: E 57 MET cc_start: 0.7878 (mpp) cc_final: 0.7636 (mpp) REVERT: E 64 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7494 (ptt90) REVERT: E 181 PHE cc_start: 0.7446 (m-80) cc_final: 0.7218 (m-80) REVERT: E 199 MET cc_start: 0.8463 (tpt) cc_final: 0.8240 (tpp) REVERT: F 130 ARG cc_start: 0.5038 (mtt180) cc_final: 0.3957 (ttt90) REVERT: F 202 ASP cc_start: 0.8326 (t70) cc_final: 0.7847 (t70) REVERT: G 32 TRP cc_start: 0.8697 (m100) cc_final: 0.8341 (m100) REVERT: G 130 ARG cc_start: 0.5242 (mtt180) cc_final: 0.3994 (ttt90) REVERT: H 199 MET cc_start: 0.8555 (tpp) cc_final: 0.8173 (tpp) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.2833 time to fit residues: 146.2646 Evaluate side-chains 247 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 214 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 221 optimal weight: 0.0470 chunk 147 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 GLN A 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.139383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.104796 restraints weight = 50108.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102661 restraints weight = 61560.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.103536 restraints weight = 56041.133| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18698 Z= 0.117 Angle : 0.583 9.111 25226 Z= 0.308 Chirality : 0.042 0.173 2826 Planarity : 0.003 0.038 3102 Dihedral : 4.721 72.281 2522 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.22 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.85 (0.18), residues: 2298 helix: 1.82 (0.15), residues: 1229 sheet: -1.11 (0.40), residues: 161 loop : -0.87 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 177 HIS 0.010 0.001 HIS B 435 PHE 0.020 0.001 PHE F 115 TYR 0.021 0.001 TYR C 732 ARG 0.007 0.000 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 952) hydrogen bonds : angle 4.27689 ( 2724) SS BOND : bond 0.00106 ( 12) SS BOND : angle 1.16225 ( 24) covalent geometry : bond 0.00240 (18686) covalent geometry : angle 0.58226 (25202) *********************** 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 368 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 2.342 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 SER cc_start: 0.9385 (m) cc_final: 0.9025 (p) REVERT: A 650 LEU cc_start: 0.8521 (tp) cc_final: 0.8257 (tp) REVERT: A 670 MET cc_start: 0.9000 (mtm) cc_final: 0.7797 (tpp) REVERT: A 727 LEU cc_start: 0.8308 (mp) cc_final: 0.7802 (tp) REVERT: A 809 VAL cc_start: 0.9255 (p) cc_final: 0.8988 (t) REVERT: B 799 LEU cc_start: 0.9508 (tp) cc_final: 0.9307 (tp) REVERT: C 408 MET cc_start: 0.7329 (tpt) cc_final: 0.7042 (tpp) REVERT: C 650 LEU cc_start: 0.8247 (tp) cc_final: 0.7775 (tp) REVERT: C 670 MET cc_start: 0.9142 (mtt) cc_final: 0.8738 (mtt) REVERT: D 585 MET cc_start: 0.8921 (mmt) cc_final: 0.8668 (mmt) REVERT: D 659 PHE cc_start: 0.8145 (m-80) cc_final: 0.7722 (m-80) REVERT: D 702 TYR cc_start: 0.7332 (t80) cc_final: 0.6970 (t80) REVERT: D 788 SER cc_start: 0.8644 (p) cc_final: 0.8293 (m) REVERT: E 181 PHE cc_start: 0.7180 (m-80) cc_final: 0.6977 (m-80) REVERT: E 199 MET cc_start: 0.8345 (tpt) cc_final: 0.8132 (tpp) REVERT: F 32 TRP cc_start: 0.8523 (m100) cc_final: 0.8285 (m100) REVERT: F 130 ARG cc_start: 0.4986 (mtt180) cc_final: 0.3925 (ttt180) REVERT: F 202 ASP cc_start: 0.8090 (t70) cc_final: 0.7840 (t70) REVERT: G 32 TRP cc_start: 0.8531 (m100) cc_final: 0.8071 (m100) REVERT: G 119 LEU cc_start: 0.8732 (pp) cc_final: 0.8381 (mt) REVERT: G 130 ARG cc_start: 0.5306 (mtt180) cc_final: 0.3929 (ttt90) REVERT: H 98 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7640 (mmt90) REVERT: H 199 MET cc_start: 0.8312 (tpp) cc_final: 0.7904 (tpp) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2617 time to fit residues: 150.3760 Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 114 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN C 412 HIS ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN H 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.137903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103566 restraints weight = 50118.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101679 restraints weight = 71039.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.103045 restraints weight = 62995.610| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18698 Z= 0.131 Angle : 0.591 7.875 25226 Z= 0.312 Chirality : 0.042 0.196 2826 Planarity : 0.003 0.038 3102 Dihedral : 4.592 74.365 2522 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.66 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.87 (0.18), residues: 2298 helix: 1.79 (0.15), residues: 1229 sheet: -1.00 (0.42), residues: 150 loop : -0.81 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 177 HIS 0.009 0.001 HIS B 435 PHE 0.036 0.001 PHE G 141 TYR 0.018 0.001 TYR C 523 ARG 0.003 0.000 ARG H 5 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 952) hydrogen bonds : angle 4.30210 ( 2724) SS BOND : bond 0.00237 ( 12) SS BOND : angle 1.36178 ( 24) covalent geometry : bond 0.00282 (18686) covalent geometry : angle 0.58980 (25202) *********************** 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 333 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 2.116 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLN cc_start: 0.7006 (pt0) cc_final: 0.6438 (tm-30) REVERT: A 546 PHE cc_start: 0.8055 (t80) cc_final: 0.7825 (t80) REVERT: A 670 MET cc_start: 0.8976 (mtm) cc_final: 0.7774 (tpp) REVERT: A 727 LEU cc_start: 0.8330 (mp) cc_final: 0.7880 (tp) REVERT: A 809 VAL cc_start: 0.9251 (p) cc_final: 0.9020 (t) REVERT: C 585 MET cc_start: 0.8816 (mmt) cc_final: 0.8596 (mmt) REVERT: C 586 GLN cc_start: 0.7931 (mp10) cc_final: 0.7713 (mp10) REVERT: C 650 LEU cc_start: 0.7877 (tp) cc_final: 0.7412 (tp) REVERT: C 670 MET cc_start: 0.9074 (mtt) cc_final: 0.8258 (mmt) REVERT: D 585 MET cc_start: 0.9055 (mmt) cc_final: 0.8756 (mmt) REVERT: D 659 PHE cc_start: 0.8074 (m-80) cc_final: 0.7653 (m-80) REVERT: D 702 TYR cc_start: 0.7264 (t80) cc_final: 0.6899 (t80) REVERT: D 788 SER cc_start: 0.8724 (p) cc_final: 0.8412 (m) REVERT: F 130 ARG cc_start: 0.4973 (mtt180) cc_final: 0.3789 (ttt90) REVERT: F 202 ASP cc_start: 0.8095 (t70) cc_final: 0.7777 (t70) REVERT: G 119 LEU cc_start: 0.8705 (pp) cc_final: 0.8290 (mp) REVERT: G 130 ARG cc_start: 0.5283 (mtt180) cc_final: 0.3880 (ttt90) REVERT: H 199 MET cc_start: 0.8363 (tpp) cc_final: 0.7934 (tpp) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2660 time to fit residues: 138.8833 Evaluate side-chains 245 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.137841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103729 restraints weight = 50329.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103603 restraints weight = 74642.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104461 restraints weight = 59634.051| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18698 Z= 0.135 Angle : 0.599 8.622 25226 Z= 0.316 Chirality : 0.042 0.206 2826 Planarity : 0.003 0.042 3102 Dihedral : 4.589 76.788 2522 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.52 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.82 (0.18), residues: 2298 helix: 1.72 (0.15), residues: 1230 sheet: -1.19 (0.39), residues: 169 loop : -0.74 (0.22), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 177 HIS 0.010 0.001 HIS B 435 PHE 0.019 0.001 PHE F 96 TYR 0.018 0.001 TYR C 523 ARG 0.003 0.000 ARG H 5 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 952) hydrogen bonds : angle 4.30597 ( 2724) SS BOND : bond 0.00241 ( 12) SS BOND : angle 1.39404 ( 24) covalent geometry : bond 0.00292 (18686) covalent geometry : angle 0.59753 (25202) *********************** 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 332 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 2.313 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 PHE cc_start: 0.8076 (t80) cc_final: 0.7839 (t80) REVERT: A 650 LEU cc_start: 0.8236 (tp) cc_final: 0.7915 (tp) REVERT: A 670 MET cc_start: 0.8933 (mtm) cc_final: 0.7903 (tpp) REVERT: A 727 LEU cc_start: 0.8261 (mp) cc_final: 0.7905 (tp) REVERT: A 809 VAL cc_start: 0.9249 (p) cc_final: 0.9029 (t) REVERT: B 788 SER cc_start: 0.8872 (p) cc_final: 0.8207 (m) REVERT: C 586 GLN cc_start: 0.7894 (mp10) cc_final: 0.7606 (mp10) REVERT: C 670 MET cc_start: 0.9099 (mtt) cc_final: 0.8219 (mmt) REVERT: D 503 MET cc_start: 0.7694 (ttm) cc_final: 0.7409 (ttp) REVERT: D 585 MET cc_start: 0.8978 (mmt) cc_final: 0.8596 (mmt) REVERT: D 659 PHE cc_start: 0.8000 (m-80) cc_final: 0.7563 (m-80) REVERT: D 702 TYR cc_start: 0.7263 (t80) cc_final: 0.6862 (t80) REVERT: D 788 SER cc_start: 0.8712 (p) cc_final: 0.8462 (m) REVERT: E 181 PHE cc_start: 0.7245 (m-80) cc_final: 0.6818 (m-80) REVERT: F 130 ARG cc_start: 0.4966 (mtt180) cc_final: 0.3879 (ttt90) REVERT: G 130 ARG cc_start: 0.5326 (mtt180) cc_final: 0.3834 (ttt90) REVERT: G 186 PHE cc_start: 0.8155 (t80) cc_final: 0.7942 (t80) REVERT: H 199 MET cc_start: 0.8300 (tpp) cc_final: 0.7924 (tpp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2945 time to fit residues: 153.3404 Evaluate side-chains 244 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.137315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102741 restraints weight = 50100.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.102851 restraints weight = 68496.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103740 restraints weight = 53556.612| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18698 Z= 0.138 Angle : 0.611 8.782 25226 Z= 0.322 Chirality : 0.043 0.201 2826 Planarity : 0.003 0.045 3102 Dihedral : 4.569 78.552 2522 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.61 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.75 (0.18), residues: 2298 helix: 1.68 (0.15), residues: 1232 sheet: -1.10 (0.42), residues: 159 loop : -0.85 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 177 HIS 0.008 0.001 HIS B 435 PHE 0.034 0.001 PHE G 141 TYR 0.021 0.001 TYR C 523 ARG 0.005 0.000 ARG C 715 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 952) hydrogen bonds : angle 4.37298 ( 2724) SS BOND : bond 0.00249 ( 12) SS BOND : angle 1.35832 ( 24) covalent geometry : bond 0.00301 (18686) covalent geometry : angle 0.61014 (25202) *********************** 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 328 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 2.334 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: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.6255 (tpt) cc_final: 0.5757 (tpt) REVERT: A 546 PHE cc_start: 0.8121 (t80) cc_final: 0.7918 (t80) REVERT: A 650 LEU cc_start: 0.8230 (tp) cc_final: 0.7993 (tp) REVERT: A 670 MET cc_start: 0.8968 (mtm) cc_final: 0.7555 (mmm) REVERT: A 727 LEU cc_start: 0.8319 (mp) cc_final: 0.7965 (tp) REVERT: A 809 VAL cc_start: 0.9281 (p) cc_final: 0.9075 (t) REVERT: B 592 SER cc_start: 0.9440 (t) cc_final: 0.9208 (t) REVERT: B 788 SER cc_start: 0.8839 (p) cc_final: 0.8146 (m) REVERT: C 585 MET cc_start: 0.8597 (mmt) cc_final: 0.8385 (mmt) REVERT: C 586 GLN cc_start: 0.7929 (mp10) cc_final: 0.7699 (mp10) REVERT: C 650 LEU cc_start: 0.7836 (tp) cc_final: 0.7345 (tp) REVERT: D 659 PHE cc_start: 0.7970 (m-80) cc_final: 0.7530 (m-80) REVERT: D 788 SER cc_start: 0.8712 (p) cc_final: 0.8465 (m) REVERT: F 31 TYR cc_start: 0.7169 (m-10) cc_final: 0.6936 (m-80) REVERT: F 130 ARG cc_start: 0.5086 (mtt180) cc_final: 0.4028 (ttt180) REVERT: F 202 ASP cc_start: 0.8063 (t70) cc_final: 0.7712 (t70) REVERT: G 130 ARG cc_start: 0.5369 (mtt180) cc_final: 0.3826 (ttt90) REVERT: H 199 MET cc_start: 0.8302 (tpp) cc_final: 0.7914 (tpp) REVERT: H 203 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.7316 (ttt180) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2721 time to fit residues: 139.8065 Evaluate side-chains 242 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 42 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 198 optimal weight: 0.4980 chunk 113 optimal weight: 0.0770 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.133785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099838 restraints weight = 49254.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099257 restraints weight = 74029.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.100156 restraints weight = 58266.860| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18698 Z= 0.210 Angle : 0.681 9.122 25226 Z= 0.366 Chirality : 0.045 0.277 2826 Planarity : 0.004 0.048 3102 Dihedral : 4.873 80.306 2522 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.05 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.47 (0.18), residues: 2298 helix: 1.45 (0.15), residues: 1221 sheet: -1.17 (0.43), residues: 148 loop : -0.96 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 177 HIS 0.011 0.001 HIS H 131 PHE 0.029 0.002 PHE E 200 TYR 0.029 0.002 TYR B 702 ARG 0.004 0.000 ARG H 5 Details of bonding type rmsd hydrogen bonds : bond 0.05620 ( 952) hydrogen bonds : angle 4.68825 ( 2724) SS BOND : bond 0.00393 ( 12) SS BOND : angle 1.40354 ( 24) covalent geometry : bond 0.00465 (18686) covalent geometry : angle 0.67987 (25202) ********************** 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 312 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 2.236 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.6442 (tpt) cc_final: 0.6078 (tpt) REVERT: A 428 LEU cc_start: 0.8411 (tp) cc_final: 0.8138 (tt) REVERT: A 670 MET cc_start: 0.8958 (mtm) cc_final: 0.7985 (tpp) REVERT: A 727 LEU cc_start: 0.8273 (mp) cc_final: 0.7986 (tp) REVERT: A 809 VAL cc_start: 0.9343 (p) cc_final: 0.9121 (t) REVERT: B 463 MET cc_start: 0.5850 (mpp) cc_final: 0.5295 (mpp) REVERT: B 788 SER cc_start: 0.8849 (p) cc_final: 0.8114 (m) REVERT: C 408 MET cc_start: 0.7715 (tpt) cc_final: 0.6876 (tpt) REVERT: C 585 MET cc_start: 0.8576 (mmt) cc_final: 0.8316 (mmm) REVERT: C 586 GLN cc_start: 0.7992 (mp10) cc_final: 0.7736 (mp10) REVERT: C 721 MET cc_start: 0.8414 (ppp) cc_final: 0.8095 (ppp) REVERT: D 585 MET cc_start: 0.9027 (mmt) cc_final: 0.8809 (tpp) REVERT: D 659 PHE cc_start: 0.7767 (m-80) cc_final: 0.7390 (m-80) REVERT: D 788 SER cc_start: 0.8652 (p) cc_final: 0.8412 (m) REVERT: F 31 TYR cc_start: 0.7347 (m-10) cc_final: 0.7080 (m-80) REVERT: F 126 PHE cc_start: 0.7400 (p90) cc_final: 0.7166 (p90) REVERT: F 130 ARG cc_start: 0.5064 (mtt180) cc_final: 0.4025 (ttt180) REVERT: F 188 ILE cc_start: 0.8786 (mp) cc_final: 0.8488 (mp) REVERT: G 130 ARG cc_start: 0.5237 (mtt180) cc_final: 0.3685 (ttt90) REVERT: H 199 MET cc_start: 0.8295 (tpp) cc_final: 0.7923 (tpp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2767 time to fit residues: 134.7576 Evaluate side-chains 233 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 66 optimal weight: 2.9990 chunk 151 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 95 optimal weight: 0.0670 chunk 172 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS G 148 ASN H 131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.136933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103679 restraints weight = 50135.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.101282 restraints weight = 74086.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102112 restraints weight = 68044.320| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18698 Z= 0.126 Angle : 0.620 8.935 25226 Z= 0.324 Chirality : 0.043 0.202 2826 Planarity : 0.003 0.051 3102 Dihedral : 4.618 79.457 2522 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.57 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.70 (0.18), residues: 2298 helix: 1.70 (0.15), residues: 1215 sheet: -1.18 (0.43), residues: 147 loop : -0.90 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP H 177 HIS 0.006 0.001 HIS H 131 PHE 0.028 0.001 PHE G 140 TYR 0.020 0.001 TYR C 523 ARG 0.003 0.000 ARG H 5 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 952) hydrogen bonds : angle 4.37277 ( 2724) SS BOND : bond 0.00292 ( 12) SS BOND : angle 1.25991 ( 24) covalent geometry : bond 0.00265 (18686) covalent geometry : angle 0.61899 (25202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5798.58 seconds wall clock time: 102 minutes 53.47 seconds (6173.47 seconds total)