Starting phenix.real_space_refine on Mon Jun 16 06:58:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dht_46876/06_2025/9dht_46876.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dht_46876/06_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_46876/06_2025/9dht_46876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dht_46876/06_2025/9dht_46876.map" model { file = "/net/cci-nas-00/data/ceres_data/9dht_46876/06_2025/9dht_46876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dht_46876/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.14, per 1000 atoms: 0.66 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: 4.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 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: 1.86 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: 5.82 Time building geometry restraints manager: 5.67 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: 6.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.630 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.330 ------------------------------------------------------------------------------- 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 : 2.044 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: 0.3182 time to fit residues: 293.0730 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 : 1.933 ------------------------------------------------------------------------------- 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 = 0.105521 restraints weight = 49188.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104494 restraints weight = 67928.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105107 restraints weight = 60078.174| |-----------------------------------------------------------------------------| 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 2.76877 ( 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 : 1.851 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: 0.6652 (m-80) cc_final: 0.5875 (m-10) REVERT: A 496 MET cc_start: 0.5167 (ttp) cc_final: 0.4948 (ttp) REVERT: A 576 SER cc_start: 0.9528 (m) cc_final: 0.9306 (p) REVERT: A 708 MET cc_start: 0.8166 (mtt) cc_final: 0.7567 (mtt) REVERT: B 503 MET cc_start: 0.7831 (ttm) cc_final: 0.7427 (ttm) REVERT: B 544 SER cc_start: 0.9258 (m) cc_final: 0.8954 (p) REVERT: B 573 ILE cc_start: 0.9379 (tp) cc_final: 0.8862 (tt) REVERT: B 577 LEU cc_start: 0.9316 (mt) cc_final: 0.9114 (mt) REVERT: B 702 TYR cc_start: 0.7007 (t80) cc_final: 0.6727 (t80) REVERT: B 708 MET cc_start: 0.8093 (mpp) cc_final: 0.7818 (mpp) REVERT: C 491 PHE cc_start: 0.6988 (m-80) cc_final: 0.6783 (m-10) REVERT: C 576 SER cc_start: 0.9656 (m) cc_final: 0.9448 (p) REVERT: C 650 LEU cc_start: 0.8368 (tp) cc_final: 0.7736 (tp) REVERT: C 670 MET cc_start: 0.9177 (mtt) cc_final: 0.8600 (mtt) REVERT: C 708 MET cc_start: 0.8250 (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: 0.9073 (mmt) cc_final: 0.8854 (mmt) REVERT: E 81 HIS cc_start: 0.7753 (m90) cc_final: 0.7532 (m-70) REVERT: E 181 PHE cc_start: 0.7710 (m-80) cc_final: 0.7451 (m-80) REVERT: E 199 MET cc_start: 0.8366 (tpt) cc_final: 0.8076 (tpp) REVERT: F 130 ARG cc_start: 0.4921 (mtt180) cc_final: 0.3888 (ttt180) REVERT: F 187 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8236 (mm) REVERT: F 188 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8537 (mp) REVERT: F 197 VAL cc_start: 0.9529 (t) cc_final: 0.9287 (p) REVERT: G 130 ARG cc_start: 0.5296 (mtt180) cc_final: 0.4641 (ttt90) REVERT: H 199 MET cc_start: 0.8591 (tpp) cc_final: 0.8091 (tpp) outliers start: 2 outliers final: 0 residues processed: 394 average time/residue: 0.2990 time to fit residues: 179.9787 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 : 2.172 ------------------------------------------------------------------------------- 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: 0.9980 chunk 223 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 37 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.141737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104789 restraints weight = 48407.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101587 restraints weight = 37769.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102149 restraints weight = 38341.564| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4268 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= 0.135 Angle : 0.586 7.342 25226 Z= 0.316 Chirality : 0.042 0.172 2826 Planarity : 0.004 0.041 3102 Dihedral : 5.161 64.861 2522 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.39 % Favored : 96.39 % Rotamer: Outliers : 0.20 % Allowed : 3.12 % Favored : 96.68 % 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: 0.96 (0.18), residues: 2298 helix: 1.83 (0.15), residues: 1212 sheet: -0.95 (0.42), residues: 152 loop : -0.67 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 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 0.04842 ( 952) hydrogen bonds : angle 4.48030 ( 2724) SS BOND : bond 0.01580 ( 12) SS BOND : angle 1.42192 ( 24) covalent geometry : bond 0.00282 (18686) covalent geometry : angle 0.58454 (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 379 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 375 time to evaluate : 1.882 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: A 450 TYR cc_start: 0.6767 (m-80) cc_final: 0.5994 (m-80) REVERT: A 573 ILE cc_start: 0.9149 (tp) cc_final: 0.8945 (tp) REVERT: A 576 SER cc_start: 0.9633 (m) cc_final: 0.9345 (p) REVERT: A 587 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8005 (mp10) REVERT: A 650 LEU cc_start: 0.8489 (tp) cc_final: 0.8254 (tp) REVERT: A 670 MET cc_start: 0.8953 (mtm) cc_final: 0.8390 (mtp) REVERT: B 503 MET cc_start: 0.7627 (ttm) cc_final: 0.7356 (ttm) REVERT: B 544 SER cc_start: 0.9172 (m) cc_final: 0.8850 (p) REVERT: B 573 ILE cc_start: 0.9298 (tp) cc_final: 0.8900 (tt) REVERT: B 812 ILE cc_start: 0.8082 (tt) cc_final: 0.7839 (tt) REVERT: C 576 SER cc_start: 0.9661 (m) cc_final: 0.9392 (p) REVERT: C 650 LEU cc_start: 0.8330 (tp) cc_final: 0.7802 (tp) REVERT: C 670 MET cc_start: 0.9150 (mtt) cc_final: 0.8038 (mmp) REVERT: C 811 LEU cc_start: 0.8946 (mm) cc_final: 0.8686 (tp) REVERT: D 585 MET cc_start: 0.9091 (mmt) cc_final: 0.8866 (mmt) REVERT: D 714 GLN cc_start: 0.8543 (mp10) cc_final: 0.8026 (pm20) REVERT: D 788 SER cc_start: 0.8935 (p) cc_final: 0.8537 (m) REVERT: E 81 HIS cc_start: 0.7854 (m90) cc_final: 0.7630 (m-70) REVERT: E 199 MET cc_start: 0.8406 (tpt) cc_final: 0.8115 (tpp) REVERT: F 32 TRP cc_start: 0.8249 (m100) cc_final: 0.7990 (m100) REVERT: F 130 ARG cc_start: 0.4816 (mtt180) cc_final: 0.3717 (ttt180) REVERT: F 187 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8096 (mt) REVERT: F 188 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8649 (mp) REVERT: F 197 VAL cc_start: 0.9530 (t) cc_final: 0.9318 (p) REVERT: G 32 TRP cc_start: 0.8197 (m100) cc_final: 0.7939 (m100) REVERT: G 119 LEU cc_start: 0.8700 (pp) cc_final: 0.8393 (mp) REVERT: G 130 ARG cc_start: 0.5491 (mtt180) cc_final: 0.4565 (ttt180) REVERT: G 134 ILE cc_start: 0.7748 (mm) cc_final: 0.7353 (mm) REVERT: H 57 MET cc_start: 0.7747 (mpp) cc_final: 0.7393 (mpp) REVERT: H 199 MET cc_start: 0.8669 (tpp) cc_final: 0.8220 (tpp) outliers start: 4 outliers final: 1 residues processed: 379 average time/residue: 0.3818 time to fit residues: 223.1484 Evaluate side-chains 293 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 3.315 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 227 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.138782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103658 restraints weight = 48443.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101547 restraints weight = 51609.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102604 restraints weight = 49143.300| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4859 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= 0.160 Angle : 0.606 7.990 25226 Z= 0.326 Chirality : 0.043 0.172 2826 Planarity : 0.004 0.042 3102 Dihedral : 4.983 65.543 2522 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 0.05 % Allowed : 3.32 % 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: 0.91 (0.18), residues: 2298 helix: 1.76 (0.15), residues: 1214 sheet: -1.01 (0.41), residues: 154 loop : -0.64 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 767 HIS 0.032 0.002 HIS H 131 PHE 0.024 0.002 PHE G 140 TYR 0.026 0.002 TYR C 647 ARG 0.002 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 952) hydrogen bonds : angle 4.52077 ( 2724) SS BOND : bond 0.00282 ( 12) SS BOND : angle 1.43189 ( 24) covalent geometry : bond 0.00348 (18686) covalent geometry : angle 0.60504 (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 340 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 2.122 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 450 TYR cc_start: 0.7023 (m-80) cc_final: 0.6311 (m-80) REVERT: A 576 SER cc_start: 0.9554 (m) cc_final: 0.9216 (p) REVERT: A 670 MET cc_start: 0.8899 (mtm) cc_final: 0.7713 (tpp) REVERT: A 727 LEU cc_start: 0.8357 (mp) cc_final: 0.7756 (tp) REVERT: B 573 ILE cc_start: 0.9423 (tp) cc_final: 0.8975 (tt) REVERT: B 812 ILE cc_start: 0.8372 (tt) cc_final: 0.8132 (tt) REVERT: C 586 GLN cc_start: 0.8165 (mp10) cc_final: 0.7780 (mp10) REVERT: C 650 LEU cc_start: 0.8332 (tp) cc_final: 0.7880 (tp) REVERT: C 670 MET cc_start: 0.9172 (mtt) cc_final: 0.8804 (mtt) REVERT: C 811 LEU cc_start: 0.8870 (mm) cc_final: 0.8637 (tp) REVERT: D 585 MET cc_start: 0.9118 (mmt) cc_final: 0.8912 (mmt) REVERT: D 659 PHE cc_start: 0.8149 (m-80) cc_final: 0.7742 (m-80) REVERT: D 788 SER cc_start: 0.8729 (p) cc_final: 0.8307 (m) REVERT: D 817 LYS cc_start: 0.7940 (mttt) cc_final: 0.7411 (mttp) REVERT: E 57 MET cc_start: 0.7673 (mpp) cc_final: 0.7421 (mpp) REVERT: E 64 ARG cc_start: 0.7664 (ptt180) cc_final: 0.7239 (ptt90) REVERT: E 81 HIS cc_start: 0.7836 (m90) cc_final: 0.7607 (m-70) REVERT: E 199 MET cc_start: 0.8388 (tpt) cc_final: 0.8062 (tpp) REVERT: F 32 TRP cc_start: 0.8472 (m100) cc_final: 0.8170 (m100) REVERT: F 96 PHE cc_start: 0.6321 (t80) cc_final: 0.5950 (t80) REVERT: F 130 ARG cc_start: 0.5037 (mtt180) cc_final: 0.3870 (ttt90) REVERT: F 135 LEU cc_start: 0.8375 (tp) cc_final: 0.8146 (mt) REVERT: F 202 ASP cc_start: 0.8289 (t70) cc_final: 0.8088 (t70) REVERT: G 32 TRP cc_start: 0.8435 (m100) cc_final: 0.8080 (m100) REVERT: G 130 ARG cc_start: 0.5395 (mtt180) cc_final: 0.4216 (ttt90) REVERT: H 199 MET cc_start: 0.8555 (tpp) cc_final: 0.8081 (tpp) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.2879 time to fit residues: 151.8350 Evaluate side-chains 265 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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: 5.9990 chunk 207 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 117 optimal weight: 0.0570 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- 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** ** B 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** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.137613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104154 restraints weight = 48620.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101461 restraints weight = 49598.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102353 restraints weight = 46893.314| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18698 Z= 0.161 Angle : 0.598 7.458 25226 Z= 0.322 Chirality : 0.043 0.173 2826 Planarity : 0.004 0.051 3102 Dihedral : 4.941 72.063 2522 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % Rotamer: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % 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: 0.86 (0.18), residues: 2298 helix: 1.73 (0.15), residues: 1225 sheet: -1.02 (0.41), residues: 152 loop : -0.73 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 177 HIS 0.010 0.001 HIS B 435 PHE 0.018 0.002 PHE G 140 TYR 0.020 0.001 TYR C 647 ARG 0.016 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 952) hydrogen bonds : angle 4.45382 ( 2724) SS BOND : bond 0.00223 ( 12) SS BOND : angle 1.20267 ( 24) covalent geometry : bond 0.00355 (18686) covalent geometry : angle 0.59749 (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 338 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 1.973 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: A 450 TYR cc_start: 0.7220 (m-80) cc_final: 0.6675 (m-80) REVERT: A 670 MET cc_start: 0.8838 (mtm) cc_final: 0.8021 (tpp) REVERT: A 727 LEU cc_start: 0.8372 (mp) cc_final: 0.7869 (tp) REVERT: A 808 LEU cc_start: 0.9244 (pp) cc_final: 0.9030 (pp) REVERT: B 586 GLN cc_start: 0.8422 (mp10) cc_final: 0.8047 (mp10) REVERT: B 812 ILE cc_start: 0.8400 (tt) cc_final: 0.8174 (tt) REVERT: C 670 MET cc_start: 0.9139 (mtt) cc_final: 0.8851 (mtt) REVERT: C 811 LEU cc_start: 0.8873 (mm) cc_final: 0.8619 (tp) REVERT: D 585 MET cc_start: 0.9164 (mmt) cc_final: 0.8852 (mmt) REVERT: D 788 SER cc_start: 0.8723 (p) cc_final: 0.8320 (m) REVERT: E 181 PHE cc_start: 0.7274 (m-80) cc_final: 0.7047 (m-80) REVERT: E 199 MET cc_start: 0.8417 (tpt) cc_final: 0.8119 (tpp) REVERT: F 130 ARG cc_start: 0.5031 (mtt180) cc_final: 0.4002 (ttt90) REVERT: F 202 ASP cc_start: 0.8367 (t70) cc_final: 0.7958 (t70) REVERT: G 32 TRP cc_start: 0.8569 (m100) cc_final: 0.8135 (m100) REVERT: G 96 PHE cc_start: 0.6361 (t80) cc_final: 0.5952 (t80) REVERT: G 119 LEU cc_start: 0.8750 (pp) cc_final: 0.8395 (mt) REVERT: G 130 ARG cc_start: 0.5337 (mtt180) cc_final: 0.4026 (ttt180) REVERT: H 199 MET cc_start: 0.8541 (tpp) cc_final: 0.8163 (tpp) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.2749 time to fit residues: 143.7756 Evaluate side-chains 248 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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: 0.8980 chunk 41 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 221 optimal weight: 0.0980 chunk 147 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN ** B 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** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.138431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103421 restraints weight = 48977.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100604 restraints weight = 43576.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101067 restraints weight = 44756.045| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5634 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= 0.129 Angle : 0.587 8.903 25226 Z= 0.311 Chirality : 0.042 0.187 2826 Planarity : 0.004 0.059 3102 Dihedral : 4.701 71.632 2522 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 0.94 (0.18), residues: 2298 helix: 1.87 (0.15), residues: 1222 sheet: -1.00 (0.42), residues: 150 loop : -0.79 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 177 HIS 0.009 0.001 HIS B 435 PHE 0.028 0.001 PHE F 115 TYR 0.022 0.001 TYR B 702 ARG 0.008 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 952) hydrogen bonds : angle 4.30698 ( 2724) SS BOND : bond 0.00192 ( 12) SS BOND : angle 1.16536 ( 24) covalent geometry : bond 0.00278 (18686) covalent geometry : angle 0.58601 (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 338 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.944 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 620 LEU cc_start: 0.9268 (tp) cc_final: 0.9035 (tt) REVERT: A 670 MET cc_start: 0.9022 (mtm) cc_final: 0.7664 (tpp) REVERT: A 727 LEU cc_start: 0.8466 (mp) cc_final: 0.7990 (tp) REVERT: A 809 VAL cc_start: 0.9363 (t) cc_final: 0.9144 (p) REVERT: C 414 MET cc_start: 0.8558 (mpp) cc_final: 0.8319 (mpp) REVERT: C 585 MET cc_start: 0.8905 (mmt) cc_final: 0.8689 (mmt) REVERT: C 586 GLN cc_start: 0.8053 (mp10) cc_final: 0.7742 (mp10) REVERT: C 650 LEU cc_start: 0.8274 (tp) cc_final: 0.7722 (tp) REVERT: C 670 MET cc_start: 0.9206 (mtt) cc_final: 0.8742 (mtt) REVERT: C 811 LEU cc_start: 0.8879 (mm) cc_final: 0.8677 (tp) REVERT: D 659 PHE cc_start: 0.8192 (m-80) cc_final: 0.7752 (m-80) REVERT: D 788 SER cc_start: 0.8650 (p) cc_final: 0.8393 (m) REVERT: D 817 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7772 (mmtp) REVERT: E 156 ILE cc_start: 0.8947 (tp) cc_final: 0.8543 (mt) REVERT: E 181 PHE cc_start: 0.7404 (m-80) cc_final: 0.7200 (m-80) REVERT: F 32 TRP cc_start: 0.8532 (m100) cc_final: 0.8270 (m100) REVERT: F 130 ARG cc_start: 0.4927 (mtt180) cc_final: 0.3909 (ttt180) REVERT: F 202 ASP cc_start: 0.8292 (t70) cc_final: 0.8068 (t70) REVERT: G 130 ARG cc_start: 0.5225 (mtt180) cc_final: 0.3880 (ttt90) REVERT: H 199 MET cc_start: 0.8466 (tpp) cc_final: 0.8073 (tpp) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2819 time to fit residues: 147.4166 Evaluate side-chains 258 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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: 9.9990 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 148 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.135072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.102174 restraints weight = 50340.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100446 restraints weight = 81366.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101717 restraints weight = 68499.062| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18698 Z= 0.195 Angle : 0.664 7.922 25226 Z= 0.356 Chirality : 0.044 0.187 2826 Planarity : 0.004 0.062 3102 Dihedral : 4.909 76.472 2522 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.87 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 0.52 (0.18), residues: 2298 helix: 1.43 (0.15), residues: 1237 sheet: -1.16 (0.42), residues: 152 loop : -0.87 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 177 HIS 0.008 0.001 HIS B 435 PHE 0.028 0.002 PHE G 140 TYR 0.017 0.002 TYR E 175 ARG 0.010 0.001 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.05693 ( 952) hydrogen bonds : angle 4.73385 ( 2724) SS BOND : bond 0.00439 ( 12) SS BOND : angle 1.58171 ( 24) covalent geometry : bond 0.00429 (18686) covalent geometry : angle 0.66224 (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 315 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 2.134 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 670 MET cc_start: 0.9057 (mtm) cc_final: 0.8097 (tpp) REVERT: A 727 LEU cc_start: 0.8352 (mp) cc_final: 0.7913 (tp) REVERT: A 808 LEU cc_start: 0.9191 (pp) cc_final: 0.8925 (pp) REVERT: A 809 VAL cc_start: 0.9358 (t) cc_final: 0.9148 (p) REVERT: B 788 SER cc_start: 0.8807 (p) cc_final: 0.8099 (m) REVERT: C 586 GLN cc_start: 0.8048 (mp10) cc_final: 0.7748 (mp10) REVERT: C 811 LEU cc_start: 0.8849 (mm) cc_final: 0.8557 (tp) REVERT: D 659 PHE cc_start: 0.7882 (m-80) cc_final: 0.7485 (m-80) REVERT: D 788 SER cc_start: 0.8675 (p) cc_final: 0.8441 (m) REVERT: E 199 MET cc_start: 0.8376 (tpt) cc_final: 0.8157 (tpp) REVERT: F 130 ARG cc_start: 0.5085 (mtt180) cc_final: 0.3941 (ttt90) REVERT: F 135 LEU cc_start: 0.8356 (mt) cc_final: 0.8069 (mt) REVERT: F 202 ASP cc_start: 0.8083 (t70) cc_final: 0.7721 (t70) REVERT: G 130 ARG cc_start: 0.5282 (mtt180) cc_final: 0.3919 (ttt90) REVERT: H 12 THR cc_start: 0.8859 (m) cc_final: 0.8645 (p) REVERT: H 199 MET cc_start: 0.8323 (tpp) cc_final: 0.7973 (tpp) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2803 time to fit residues: 137.7309 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 : 1.939 ------------------------------------------------------------------------------- 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: 0.5980 chunk 208 optimal weight: 0.9980 chunk 179 optimal weight: 0.3980 chunk 154 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 ASN ** 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 = 0.4047 r_free = 0.4047 target = 0.137647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104071 restraints weight = 48213.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.101149 restraints weight = 47711.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.101594 restraints weight = 47027.581| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6301 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= 0.125 Angle : 0.604 8.496 25226 Z= 0.317 Chirality : 0.043 0.208 2826 Planarity : 0.003 0.047 3102 Dihedral : 4.654 76.331 2522 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.18 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 0.68 (0.18), residues: 2298 helix: 1.64 (0.15), residues: 1244 sheet: -1.08 (0.44), residues: 138 loop : -0.96 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 32 HIS 0.009 0.001 HIS B 435 PHE 0.018 0.001 PHE C 517 TYR 0.021 0.001 TYR B 702 ARG 0.009 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 952) hydrogen bonds : angle 4.37333 ( 2724) SS BOND : bond 0.00217 ( 12) SS BOND : angle 1.39704 ( 24) covalent geometry : bond 0.00266 (18686) covalent geometry : angle 0.60304 (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 330 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 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: A 408 MET cc_start: 0.6650 (tpt) cc_final: 0.6391 (tpt) REVERT: A 620 LEU cc_start: 0.9246 (tp) cc_final: 0.9004 (tt) REVERT: A 670 MET cc_start: 0.8998 (mtm) cc_final: 0.8058 (mmm) REVERT: A 727 LEU cc_start: 0.8458 (mp) cc_final: 0.8060 (tp) REVERT: A 808 LEU cc_start: 0.9272 (pp) cc_final: 0.9002 (pp) REVERT: A 809 VAL cc_start: 0.9320 (t) cc_final: 0.9053 (p) REVERT: B 788 SER cc_start: 0.8863 (p) cc_final: 0.8187 (m) REVERT: C 586 GLN cc_start: 0.8075 (mp10) cc_final: 0.7756 (mp10) REVERT: C 670 MET cc_start: 0.9236 (mtt) cc_final: 0.8281 (mmt) REVERT: D 659 PHE cc_start: 0.7978 (m-80) cc_final: 0.7501 (m-80) REVERT: D 788 SER cc_start: 0.8651 (p) cc_final: 0.8392 (m) REVERT: E 181 PHE cc_start: 0.7319 (m-80) cc_final: 0.6947 (m-80) REVERT: E 199 MET cc_start: 0.8391 (tpt) cc_final: 0.8036 (tpp) REVERT: F 130 ARG cc_start: 0.5112 (mtt180) cc_final: 0.3955 (ttt180) REVERT: F 135 LEU cc_start: 0.8141 (mt) cc_final: 0.7936 (mt) REVERT: G 130 ARG cc_start: 0.5243 (mtt180) cc_final: 0.3828 (ttt90) REVERT: H 12 THR cc_start: 0.8900 (m) cc_final: 0.8689 (p) REVERT: H 173 TYR cc_start: 0.8417 (p90) cc_final: 0.8216 (p90) REVERT: H 199 MET cc_start: 0.8340 (tpp) cc_final: 0.7948 (tpp) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.2825 time to fit residues: 145.8385 Evaluate side-chains 243 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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: 0.2980 chunk 208 optimal weight: 0.0770 chunk 217 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.4760 ------------------------------------------------------------------------------- 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** ** B 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** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.138365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104672 restraints weight = 48297.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100370 restraints weight = 42542.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100971 restraints weight = 45497.662| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6506 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= 0.118 Angle : 0.605 8.786 25226 Z= 0.314 Chirality : 0.042 0.200 2826 Planarity : 0.003 0.044 3102 Dihedral : 4.495 78.142 2522 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.52 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.73 (0.18), residues: 2298 helix: 1.67 (0.15), residues: 1243 sheet: -1.07 (0.41), residues: 162 loop : -0.89 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 177 HIS 0.008 0.001 HIS B 435 PHE 0.035 0.001 PHE G 141 TYR 0.021 0.001 TYR C 523 ARG 0.008 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 952) hydrogen bonds : angle 4.28672 ( 2724) SS BOND : bond 0.00204 ( 12) SS BOND : angle 1.28825 ( 24) covalent geometry : bond 0.00247 (18686) covalent geometry : angle 0.60414 (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 339 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 2.126 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 408 MET cc_start: 0.6547 (tpt) cc_final: 0.6262 (tpt) REVERT: A 585 MET cc_start: 0.8827 (tpp) cc_final: 0.8601 (tpp) REVERT: A 620 LEU cc_start: 0.9110 (tp) cc_final: 0.8880 (tt) REVERT: A 650 LEU cc_start: 0.8333 (tp) cc_final: 0.8108 (tp) REVERT: A 670 MET cc_start: 0.8948 (mtm) cc_final: 0.8301 (mmt) REVERT: A 727 LEU cc_start: 0.8395 (mp) cc_final: 0.8109 (tp) REVERT: B 463 MET cc_start: 0.5768 (mpp) cc_final: 0.5009 (mpp) REVERT: B 580 SER cc_start: 0.9530 (t) cc_final: 0.9328 (t) REVERT: B 788 SER cc_start: 0.8862 (p) cc_final: 0.8178 (m) REVERT: C 586 GLN cc_start: 0.7987 (mp10) cc_final: 0.7720 (mp10) REVERT: C 590 ASP cc_start: 0.5790 (t0) cc_final: 0.5517 (t0) REVERT: C 650 LEU cc_start: 0.7846 (tp) cc_final: 0.7414 (tp) REVERT: D 503 MET cc_start: 0.7458 (ttp) cc_final: 0.7051 (ttm) REVERT: D 659 PHE cc_start: 0.7983 (m-80) cc_final: 0.7542 (m-80) REVERT: D 788 SER cc_start: 0.8600 (p) cc_final: 0.8332 (m) REVERT: E 199 MET cc_start: 0.8288 (tpt) cc_final: 0.7973 (tpp) REVERT: F 31 TYR cc_start: 0.7075 (m-10) cc_final: 0.6856 (m-80) REVERT: F 130 ARG cc_start: 0.5143 (mtt180) cc_final: 0.3999 (ttt180) REVERT: F 202 ASP cc_start: 0.8205 (t70) cc_final: 0.7850 (t70) REVERT: G 130 ARG cc_start: 0.5312 (mtt180) cc_final: 0.3770 (ttt90) REVERT: H 12 THR cc_start: 0.8940 (m) cc_final: 0.8721 (p) REVERT: H 199 MET cc_start: 0.8299 (tpp) cc_final: 0.7876 (tpp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2986 time to fit residues: 159.4756 Evaluate side-chains 256 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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: 0.9980 chunk 171 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 203 optimal weight: 0.0670 chunk 190 optimal weight: 0.0070 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 198 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 412 HIS ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 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 = 0.4062 r_free = 0.4062 target = 0.138832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.106189 restraints weight = 49049.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103923 restraints weight = 59944.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.105012 restraints weight = 59254.777| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6678 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= 0.115 Angle : 0.606 8.805 25226 Z= 0.314 Chirality : 0.042 0.205 2826 Planarity : 0.003 0.044 3102 Dihedral : 4.458 78.855 2522 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.52 % 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: 0.76 (0.18), residues: 2298 helix: 1.71 (0.15), residues: 1237 sheet: -0.99 (0.42), residues: 157 loop : -0.91 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 766 HIS 0.007 0.001 HIS A 435 PHE 0.028 0.001 PHE G 140 TYR 0.021 0.001 TYR B 702 ARG 0.007 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 952) hydrogen bonds : angle 4.23698 ( 2724) SS BOND : bond 0.00242 ( 12) SS BOND : angle 1.23998 ( 24) covalent geometry : bond 0.00239 (18686) covalent geometry : angle 0.60465 (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 331 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 2.241 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 546 PHE cc_start: 0.7875 (t80) cc_final: 0.7664 (t80) REVERT: A 620 LEU cc_start: 0.9031 (tp) cc_final: 0.8807 (tt) REVERT: A 670 MET cc_start: 0.8871 (mtm) cc_final: 0.8021 (mmt) REVERT: A 727 LEU cc_start: 0.8244 (mp) cc_final: 0.8015 (tp) REVERT: B 463 MET cc_start: 0.5577 (mpp) cc_final: 0.4968 (mpp) REVERT: B 544 SER cc_start: 0.9114 (m) cc_final: 0.8793 (p) REVERT: B 788 SER cc_start: 0.8830 (p) cc_final: 0.8133 (m) REVERT: C 408 MET cc_start: 0.7827 (tpt) cc_final: 0.7433 (tpp) REVERT: C 590 ASP cc_start: 0.5767 (t0) cc_final: 0.5495 (t0) REVERT: C 650 LEU cc_start: 0.7694 (tp) cc_final: 0.7339 (tp) REVERT: C 721 MET cc_start: 0.8550 (ppp) cc_final: 0.8310 (ppp) REVERT: D 503 MET cc_start: 0.7299 (ttp) cc_final: 0.7008 (ttm) REVERT: D 659 PHE cc_start: 0.7735 (m-80) cc_final: 0.7380 (m-80) REVERT: D 788 SER cc_start: 0.8780 (p) cc_final: 0.8526 (m) REVERT: E 23 MET cc_start: 0.7918 (mmm) cc_final: 0.7518 (mmm) REVERT: E 199 MET cc_start: 0.8358 (tpt) cc_final: 0.8035 (tpp) REVERT: F 31 TYR cc_start: 0.7161 (m-10) cc_final: 0.6931 (m-80) REVERT: F 130 ARG cc_start: 0.5110 (mtt180) cc_final: 0.3999 (ttt180) REVERT: F 188 ILE cc_start: 0.8838 (mp) cc_final: 0.8497 (mp) REVERT: G 36 ARG cc_start: 0.7701 (mmt180) cc_final: 0.7253 (ttm-80) REVERT: G 130 ARG cc_start: 0.5320 (mtt180) cc_final: 0.3820 (ttt90) REVERT: G 180 TYR cc_start: 0.7518 (m-80) cc_final: 0.7302 (m-80) REVERT: H 199 MET cc_start: 0.8261 (tpp) cc_final: 0.7886 (tpp) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2854 time to fit residues: 149.0057 Evaluate side-chains 255 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.145 ------------------------------------------------------------------------------- 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: 1.9990 chunk 151 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 chunk 172 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 18 optimal weight: 0.0970 chunk 36 optimal weight: 0.0970 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN ** 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 = 0.4081 r_free = 0.4081 target = 0.140237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.106713 restraints weight = 51372.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105560 restraints weight = 66845.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.106563 restraints weight = 66563.757| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6853 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= 0.113 Angle : 0.599 8.419 25226 Z= 0.312 Chirality : 0.042 0.281 2826 Planarity : 0.003 0.043 3102 Dihedral : 4.360 80.353 2522 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.44 % Favored : 96.30 % 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: 0.71 (0.18), residues: 2298 helix: 1.65 (0.15), residues: 1246 sheet: -0.90 (0.46), residues: 132 loop : -0.97 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 32 HIS 0.007 0.001 HIS A 435 PHE 0.019 0.001 PHE H 115 TYR 0.016 0.001 TYR C 523 ARG 0.007 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 952) hydrogen bonds : angle 4.18371 ( 2724) SS BOND : bond 0.00240 ( 12) SS BOND : angle 1.19275 ( 24) covalent geometry : bond 0.00232 (18686) covalent geometry : angle 0.59847 (25202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5918.31 seconds wall clock time: 104 minutes 33.67 seconds (6273.67 seconds total)