Starting phenix.real_space_refine on Thu Sep 18 16:35:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dht_46876/09_2025/9dht_46876.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dht_46876/09_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_46876/09_2025/9dht_46876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dht_46876/09_2025/9dht_46876.map" model { file = "/net/cci-nas-00/data/ceres_data/9dht_46876/09_2025/9dht_46876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dht_46876/09_2025/9dht_46876.cif" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.12, per 1000 atoms: 0.23 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: 1.44 Conformation dependent library (CDL) restraints added in 719.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 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: 0.61 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: 2.85 Time building geometry restraints manager: 1.98 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 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: 6.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.890 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (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 ARG 0.018 0.002 ARG C 545 TYR 0.018 0.003 TYR C 732 PHE 0.020 0.002 PHE E 179 TRP 0.025 0.002 TRP F 63 HIS 0.003 0.001 HIS H 131 Details of bonding type rmsd covalent geometry : bond 0.00311 (18686) covalent geometry : angle 0.66492 (25202) SS BOND : bond 0.00165 ( 12) SS BOND : angle 0.57251 ( 24) hydrogen bonds : bond 0.16050 ( 952) hydrogen bonds : angle 6.13905 ( 2724) *********************** 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 : 0.672 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: 0.1307 time to fit residues: 121.4150 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** ** F 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 = 0.4090 r_free = 0.4090 target = 0.140581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105245 restraints weight = 49220.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.102069 restraints weight = 60654.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.103069 restraints weight = 54905.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103727 restraints weight = 36910.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103927 restraints weight = 34869.646| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18698 Z= 0.179 Angle : 0.657 7.574 25226 Z= 0.358 Chirality : 0.044 0.255 2826 Planarity : 0.004 0.046 3102 Dihedral : 5.711 62.989 2522 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.44 % Favored : 96.30 % Rotamer: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2298 helix: 1.47 (0.15), residues: 1197 sheet: -1.11 (0.40), residues: 154 loop : -0.70 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 684 TYR 0.018 0.002 TYR E 175 PHE 0.038 0.002 PHE G 140 TRP 0.018 0.002 TRP E 177 HIS 0.003 0.001 HIS F 131 Details of bonding type rmsd covalent geometry : bond 0.00400 (18686) covalent geometry : angle 0.65274 (25202) SS BOND : bond 0.00418 ( 12) SS BOND : angle 2.38920 ( 24) hydrogen bonds : bond 0.05801 ( 952) hydrogen bonds : angle 4.95179 ( 2724) *********************** 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 392 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 390 time to evaluate : 0.617 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: A 450 TYR cc_start: 0.6559 (m-80) cc_final: 0.5782 (m-10) REVERT: A 496 MET cc_start: 0.5042 (ttp) cc_final: 0.4774 (ttp) REVERT: A 503 MET cc_start: 0.7372 (tmm) cc_final: 0.7145 (tmm) REVERT: A 576 SER cc_start: 0.9538 (m) cc_final: 0.9325 (p) REVERT: A 708 MET cc_start: 0.8254 (mtt) cc_final: 0.7660 (mtt) REVERT: A 728 ASP cc_start: 0.8353 (t70) cc_final: 0.8127 (t0) REVERT: B 503 MET cc_start: 0.7846 (ttm) cc_final: 0.7435 (ttm) REVERT: B 544 SER cc_start: 0.9218 (m) cc_final: 0.8925 (p) REVERT: B 573 ILE cc_start: 0.9370 (tp) cc_final: 0.8846 (tt) REVERT: B 702 TYR cc_start: 0.6969 (t80) cc_final: 0.6734 (t80) REVERT: B 708 MET cc_start: 0.8108 (mpp) cc_final: 0.7818 (mpp) REVERT: C 491 PHE cc_start: 0.7043 (m-80) cc_final: 0.6826 (m-10) REVERT: C 576 SER cc_start: 0.9617 (m) cc_final: 0.9398 (p) REVERT: C 650 LEU cc_start: 0.8411 (tp) cc_final: 0.7746 (tp) REVERT: C 670 MET cc_start: 0.9182 (mtt) cc_final: 0.8569 (mtt) REVERT: C 811 LEU cc_start: 0.8889 (mm) cc_final: 0.8609 (tp) REVERT: D 576 SER cc_start: 0.8709 (m) cc_final: 0.8501 (t) REVERT: D 585 MET cc_start: 0.9100 (mmt) cc_final: 0.8850 (mmt) REVERT: E 81 HIS cc_start: 0.7737 (m90) cc_final: 0.7508 (m-70) REVERT: E 181 PHE cc_start: 0.7647 (m-80) cc_final: 0.7415 (m-80) REVERT: E 199 MET cc_start: 0.8342 (tpt) cc_final: 0.8057 (tpp) REVERT: F 31 TYR cc_start: 0.6971 (m-10) cc_final: 0.6706 (m-80) REVERT: F 69 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7460 (mp0) REVERT: F 130 ARG cc_start: 0.4929 (mtt180) cc_final: 0.3848 (ttt180) REVERT: F 187 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8256 (mm) REVERT: F 188 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8529 (mp) REVERT: F 197 VAL cc_start: 0.9519 (t) cc_final: 0.9279 (p) REVERT: G 130 ARG cc_start: 0.5326 (mtt180) cc_final: 0.4625 (ttt90) REVERT: G 140 PHE cc_start: 0.8138 (m-80) cc_final: 0.7815 (m-80) REVERT: H 57 MET cc_start: 0.7736 (mpp) cc_final: 0.7468 (mpp) REVERT: H 199 MET cc_start: 0.8592 (tpp) cc_final: 0.8054 (tpp) outliers start: 2 outliers final: 0 residues processed: 392 average time/residue: 0.1201 time to fit residues: 72.2556 Evaluate side-chains 294 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 123 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 587 GLN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.138400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106835 restraints weight = 49005.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.102924 restraints weight = 56890.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104015 restraints weight = 53630.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104457 restraints weight = 35734.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.105303 restraints weight = 32991.145| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18698 Z= 0.183 Angle : 0.628 9.211 25226 Z= 0.342 Chirality : 0.044 0.172 2826 Planarity : 0.004 0.043 3102 Dihedral : 5.345 66.078 2522 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.04 % Rotamer: Outliers : 0.15 % Allowed : 3.43 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 2298 helix: 1.54 (0.15), residues: 1222 sheet: -1.03 (0.42), residues: 153 loop : -0.76 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 692 TYR 0.022 0.002 TYR E 31 PHE 0.022 0.002 PHE H 96 TRP 0.037 0.002 TRP E 177 HIS 0.006 0.001 HIS F 131 Details of bonding type rmsd covalent geometry : bond 0.00403 (18686) covalent geometry : angle 0.62641 (25202) SS BOND : bond 0.00467 ( 12) SS BOND : angle 1.61810 ( 24) hydrogen bonds : bond 0.05534 ( 952) hydrogen bonds : angle 4.72460 ( 2724) *********************** 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 367 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 364 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.6943 (m-80) cc_final: 0.6206 (m-80) REVERT: A 503 MET cc_start: 0.7292 (tmm) cc_final: 0.7042 (tmm) REVERT: A 670 MET cc_start: 0.8909 (mtm) cc_final: 0.7602 (tpp) REVERT: B 544 SER cc_start: 0.9173 (m) cc_final: 0.8904 (p) REVERT: B 573 ILE cc_start: 0.9341 (tp) cc_final: 0.8894 (tt) REVERT: B 812 ILE cc_start: 0.8326 (tt) cc_final: 0.8025 (tt) REVERT: C 576 SER cc_start: 0.9672 (m) cc_final: 0.9357 (p) REVERT: C 650 LEU cc_start: 0.8346 (tp) cc_final: 0.7776 (tp) REVERT: C 670 MET cc_start: 0.9145 (mtt) cc_final: 0.8006 (mmp) REVERT: C 708 MET cc_start: 0.8324 (mtt) cc_final: 0.8058 (mtt) REVERT: C 811 LEU cc_start: 0.8983 (mm) cc_final: 0.8656 (tp) REVERT: D 585 MET cc_start: 0.9146 (mmt) cc_final: 0.8851 (mmt) REVERT: D 702 TYR cc_start: 0.7418 (t80) cc_final: 0.7168 (t80) REVERT: D 714 GLN cc_start: 0.8543 (mp10) cc_final: 0.8099 (pm20) REVERT: D 788 SER cc_start: 0.8734 (p) cc_final: 0.8327 (m) REVERT: E 64 ARG cc_start: 0.7709 (ptt180) cc_final: 0.7320 (ptt90) REVERT: E 81 HIS cc_start: 0.7699 (m90) cc_final: 0.7477 (m-70) REVERT: E 108 ILE cc_start: 0.7966 (mp) cc_final: 0.7765 (mt) REVERT: E 199 MET cc_start: 0.8399 (tpt) cc_final: 0.8089 (tpp) REVERT: F 130 ARG cc_start: 0.4975 (mtt180) cc_final: 0.3834 (ttt90) REVERT: F 187 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8184 (mt) REVERT: F 197 VAL cc_start: 0.9531 (t) cc_final: 0.9324 (p) REVERT: G 119 LEU cc_start: 0.8685 (pp) cc_final: 0.8400 (mp) REVERT: G 130 ARG cc_start: 0.5510 (mtt180) cc_final: 0.4530 (ttt180) REVERT: G 134 ILE cc_start: 0.7713 (mm) cc_final: 0.7271 (mm) REVERT: H 57 MET cc_start: 0.7676 (mpp) cc_final: 0.7446 (mpp) REVERT: H 121 ILE cc_start: 0.8717 (pt) cc_final: 0.8354 (mt) REVERT: H 177 TRP cc_start: 0.7173 (p90) cc_final: 0.5515 (m100) REVERT: H 181 PHE cc_start: 0.7828 (m-10) cc_final: 0.7424 (m-10) REVERT: H 199 MET cc_start: 0.8612 (tpp) cc_final: 0.8186 (tpp) outliers start: 3 outliers final: 0 residues processed: 367 average time/residue: 0.1202 time to fit residues: 67.7767 Evaluate side-chains 275 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 114 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 125 optimal weight: 0.0040 chunk 123 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN ** C 586 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.137481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103620 restraints weight = 50584.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.102494 restraints weight = 68996.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103589 restraints weight = 54953.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.104019 restraints weight = 36651.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104462 restraints weight = 35345.462| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 18698 Z= 0.182 Angle : 0.626 9.145 25226 Z= 0.338 Chirality : 0.043 0.172 2826 Planarity : 0.004 0.040 3102 Dihedral : 5.162 67.246 2522 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.57 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2298 helix: 1.62 (0.15), residues: 1217 sheet: -1.21 (0.40), residues: 158 loop : -0.72 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 715 TYR 0.022 0.002 TYR B 450 PHE 0.024 0.002 PHE G 140 TRP 0.019 0.001 TRP E 177 HIS 0.013 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00406 (18686) covalent geometry : angle 0.62459 (25202) SS BOND : bond 0.00296 ( 12) SS BOND : angle 1.49440 ( 24) hydrogen bonds : bond 0.05382 ( 952) hydrogen bonds : angle 4.63927 ( 2724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7187 (m-80) cc_final: 0.6598 (m-80) REVERT: A 503 MET cc_start: 0.7361 (tmm) cc_final: 0.7155 (tmm) REVERT: A 670 MET cc_start: 0.8853 (mtm) cc_final: 0.7934 (tpp) REVERT: A 727 LEU cc_start: 0.8369 (mp) cc_final: 0.7856 (tp) REVERT: A 809 VAL cc_start: 0.9263 (p) cc_final: 0.8990 (t) REVERT: B 573 ILE cc_start: 0.9447 (tp) cc_final: 0.9014 (tt) REVERT: B 702 TYR cc_start: 0.7386 (t80) cc_final: 0.7102 (t80) REVERT: B 812 ILE cc_start: 0.8374 (tt) cc_final: 0.8146 (tt) REVERT: C 670 MET cc_start: 0.9145 (mtt) cc_final: 0.8056 (mmp) REVERT: C 811 LEU cc_start: 0.8891 (mm) cc_final: 0.8622 (tp) REVERT: D 585 MET cc_start: 0.9092 (mmt) cc_final: 0.8720 (mmt) REVERT: D 659 PHE cc_start: 0.8140 (m-80) cc_final: 0.7747 (m-80) REVERT: D 788 SER cc_start: 0.8695 (p) cc_final: 0.8310 (m) REVERT: D 803 LEU cc_start: 0.8868 (tp) cc_final: 0.8657 (tp) REVERT: E 23 MET cc_start: 0.8126 (mmm) cc_final: 0.7905 (tpp) REVERT: E 57 MET cc_start: 0.7721 (mpp) cc_final: 0.7453 (mpp) REVERT: E 64 ARG cc_start: 0.7868 (ptt180) cc_final: 0.7448 (ptt90) REVERT: E 199 MET cc_start: 0.8432 (tpt) cc_final: 0.8118 (tpp) REVERT: F 130 ARG cc_start: 0.5038 (mtt180) cc_final: 0.3892 (ttt90) REVERT: F 202 ASP cc_start: 0.8244 (t70) cc_final: 0.7927 (t70) REVERT: G 69 GLU cc_start: 0.7821 (mp0) cc_final: 0.7423 (mp0) REVERT: G 130 ARG cc_start: 0.5369 (mtt180) cc_final: 0.4080 (ttt90) REVERT: G 188 ILE cc_start: 0.8647 (mt) cc_final: 0.8421 (mt) REVERT: H 199 MET cc_start: 0.8558 (tpp) cc_final: 0.7725 (tpp) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1140 time to fit residues: 61.2102 Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 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** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN G 148 ASN ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.138583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104152 restraints weight = 50927.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.102482 restraints weight = 69272.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103693 restraints weight = 63097.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.103282 restraints weight = 44008.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.104369 restraints weight = 38915.856| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18698 Z= 0.136 Angle : 0.582 7.526 25226 Z= 0.312 Chirality : 0.042 0.173 2826 Planarity : 0.003 0.039 3102 Dihedral : 4.904 72.368 2522 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.35 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2298 helix: 1.73 (0.15), residues: 1235 sheet: -1.16 (0.41), residues: 152 loop : -0.82 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 101 TYR 0.020 0.001 TYR C 732 PHE 0.022 0.001 PHE A 659 TRP 0.045 0.001 TRP E 177 HIS 0.011 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00294 (18686) covalent geometry : angle 0.58097 (25202) SS BOND : bond 0.00379 ( 12) SS BOND : angle 1.39631 ( 24) hydrogen bonds : bond 0.04808 ( 952) hydrogen bonds : angle 4.40810 ( 2724) *********************** 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 353 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.632 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 503 MET cc_start: 0.7123 (tmm) cc_final: 0.6869 (tmm) REVERT: A 576 SER cc_start: 0.9496 (m) cc_final: 0.9060 (p) REVERT: A 585 MET cc_start: 0.8816 (tpp) cc_final: 0.8610 (tpp) REVERT: A 670 MET cc_start: 0.8880 (mtm) cc_final: 0.7921 (tpp) REVERT: A 727 LEU cc_start: 0.8432 (mp) cc_final: 0.7950 (tp) REVERT: A 809 VAL cc_start: 0.9239 (p) cc_final: 0.8992 (t) REVERT: B 580 SER cc_start: 0.9568 (t) cc_final: 0.9357 (t) REVERT: B 702 TYR cc_start: 0.7260 (t80) cc_final: 0.6916 (t80) REVERT: C 408 MET cc_start: 0.7209 (tpt) cc_final: 0.6931 (tpp) REVERT: C 670 MET cc_start: 0.9082 (mtt) cc_final: 0.8065 (mmp) REVERT: D 659 PHE cc_start: 0.8080 (m-80) cc_final: 0.7643 (m-80) REVERT: D 788 SER cc_start: 0.8695 (p) cc_final: 0.8333 (m) REVERT: D 817 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7803 (mmtp) REVERT: E 23 MET cc_start: 0.8128 (mmm) cc_final: 0.7883 (tpp) REVERT: E 199 MET cc_start: 0.8412 (tpt) cc_final: 0.8127 (tpp) REVERT: F 130 ARG cc_start: 0.5065 (mtt180) cc_final: 0.4013 (ttt90) REVERT: F 135 LEU cc_start: 0.8421 (mt) cc_final: 0.8190 (mt) REVERT: G 130 ARG cc_start: 0.5335 (mtt180) cc_final: 0.3995 (ttt180) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1108 time to fit residues: 61.7070 Evaluate side-chains 257 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 22 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 117 optimal weight: 0.1980 chunk 94 optimal weight: 0.0370 chunk 200 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.138643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104001 restraints weight = 50337.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.102846 restraints weight = 68216.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103756 restraints weight = 64302.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103511 restraints weight = 44203.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.104220 restraints weight = 39317.834| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5706 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= 0.130 Angle : 0.577 8.321 25226 Z= 0.307 Chirality : 0.042 0.173 2826 Planarity : 0.003 0.039 3102 Dihedral : 4.764 75.408 2522 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.18), residues: 2298 helix: 1.72 (0.15), residues: 1243 sheet: -1.24 (0.41), residues: 153 loop : -0.82 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 5 TYR 0.019 0.001 TYR C 732 PHE 0.026 0.001 PHE F 115 TRP 0.017 0.001 TRP A 671 HIS 0.011 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00281 (18686) covalent geometry : angle 0.57562 (25202) SS BOND : bond 0.00276 ( 12) SS BOND : angle 1.22673 ( 24) hydrogen bonds : bond 0.04592 ( 952) hydrogen bonds : angle 4.28588 ( 2724) *********************** 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 351 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.5872 (ttp) cc_final: 0.5644 (ttp) REVERT: A 503 MET cc_start: 0.7099 (tmm) cc_final: 0.6851 (tmm) REVERT: A 576 SER cc_start: 0.9505 (m) cc_final: 0.9081 (p) REVERT: A 670 MET cc_start: 0.8899 (mtm) cc_final: 0.7202 (mmm) REVERT: A 727 LEU cc_start: 0.8352 (mp) cc_final: 0.7990 (tp) REVERT: B 573 ILE cc_start: 0.9325 (tp) cc_final: 0.9081 (tt) REVERT: C 590 ASP cc_start: 0.5897 (t0) cc_final: 0.5681 (t0) REVERT: C 650 LEU cc_start: 0.8327 (tp) cc_final: 0.7821 (tp) REVERT: C 670 MET cc_start: 0.9113 (mtt) cc_final: 0.8037 (mmp) REVERT: D 659 PHE cc_start: 0.8001 (m-80) cc_final: 0.7630 (m-80) REVERT: D 788 SER cc_start: 0.8671 (p) cc_final: 0.8422 (m) REVERT: D 817 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7649 (mmtp) REVERT: E 181 PHE cc_start: 0.7206 (m-80) cc_final: 0.6964 (m-80) REVERT: F 63 TRP cc_start: 0.8207 (m100) cc_final: 0.8003 (m100) REVERT: F 130 ARG cc_start: 0.4968 (mtt180) cc_final: 0.3868 (ttt90) REVERT: G 119 LEU cc_start: 0.8640 (pp) cc_final: 0.8336 (mt) REVERT: G 130 ARG cc_start: 0.5245 (mtt180) cc_final: 0.3876 (ttt90) REVERT: H 177 TRP cc_start: 0.6951 (p90) cc_final: 0.5141 (m100) REVERT: H 181 PHE cc_start: 0.7650 (m-10) cc_final: 0.7327 (m-10) REVERT: H 199 MET cc_start: 0.8404 (tpp) cc_final: 0.8114 (tpp) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1093 time to fit residues: 59.3642 Evaluate side-chains 264 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 179 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 141 optimal weight: 0.0670 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.137264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.103740 restraints weight = 50365.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.102933 restraints weight = 77633.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.103988 restraints weight = 67524.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103949 restraints weight = 46901.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104840 restraints weight = 40729.641| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6020 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= 0.149 Angle : 0.598 7.774 25226 Z= 0.318 Chirality : 0.042 0.186 2826 Planarity : 0.004 0.040 3102 Dihedral : 4.691 77.943 2522 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2298 helix: 1.73 (0.15), residues: 1235 sheet: -1.27 (0.41), residues: 158 loop : -0.83 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 203 TYR 0.019 0.001 TYR C 732 PHE 0.019 0.002 PHE C 517 TRP 0.019 0.001 TRP E 177 HIS 0.010 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00328 (18686) covalent geometry : angle 0.59684 (25202) SS BOND : bond 0.00345 ( 12) SS BOND : angle 1.54629 ( 24) hydrogen bonds : bond 0.04809 ( 952) hydrogen bonds : angle 4.35118 ( 2724) *********************** 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 326 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.631 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 496 MET cc_start: 0.5859 (ttp) cc_final: 0.5646 (ttp) REVERT: A 670 MET cc_start: 0.8939 (mtm) cc_final: 0.7482 (tpp) REVERT: A 705 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8021 (mp0) REVERT: A 727 LEU cc_start: 0.8317 (mp) cc_final: 0.8079 (tp) REVERT: A 808 LEU cc_start: 0.9257 (pp) cc_final: 0.9007 (pp) REVERT: B 463 MET cc_start: 0.5766 (mpp) cc_final: 0.4806 (mpp) REVERT: B 573 ILE cc_start: 0.9365 (tp) cc_final: 0.9063 (tt) REVERT: B 788 SER cc_start: 0.8836 (p) cc_final: 0.8175 (m) REVERT: C 585 MET cc_start: 0.8850 (mmm) cc_final: 0.8632 (mmt) REVERT: C 650 LEU cc_start: 0.8025 (tp) cc_final: 0.7805 (tp) REVERT: C 670 MET cc_start: 0.9048 (mtt) cc_final: 0.8050 (mmp) REVERT: D 659 PHE cc_start: 0.8022 (m-80) cc_final: 0.7610 (m-80) REVERT: D 788 SER cc_start: 0.8680 (p) cc_final: 0.8474 (m) REVERT: E 181 PHE cc_start: 0.7352 (m-80) cc_final: 0.7063 (m-80) REVERT: E 199 MET cc_start: 0.8327 (tpt) cc_final: 0.8009 (tpp) REVERT: F 31 TYR cc_start: 0.7079 (m-10) cc_final: 0.6868 (m-80) REVERT: F 130 ARG cc_start: 0.4966 (mtt180) cc_final: 0.3920 (ttt180) REVERT: G 130 ARG cc_start: 0.5299 (mtt180) cc_final: 0.3858 (ttt90) REVERT: H 199 MET cc_start: 0.8305 (tpp) cc_final: 0.7836 (tpp) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1308 time to fit residues: 67.0674 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 : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN H 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.134599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100564 restraints weight = 50277.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.101535 restraints weight = 75388.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.102220 restraints weight = 62153.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101934 restraints weight = 46445.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.102770 restraints weight = 38996.439| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6353 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= 0.200 Angle : 0.659 8.795 25226 Z= 0.353 Chirality : 0.044 0.212 2826 Planarity : 0.004 0.048 3102 Dihedral : 4.871 78.836 2522 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.26 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 2298 helix: 1.45 (0.15), residues: 1238 sheet: -1.39 (0.39), residues: 170 loop : -0.88 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 36 TYR 0.021 0.002 TYR C 523 PHE 0.030 0.002 PHE F 115 TRP 0.021 0.002 TRP H 177 HIS 0.009 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00441 (18686) covalent geometry : angle 0.65741 (25202) SS BOND : bond 0.00218 ( 12) SS BOND : angle 1.56886 ( 24) hydrogen bonds : bond 0.05506 ( 952) hydrogen bonds : angle 4.64639 ( 2724) *********************** 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 306 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.784 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 670 MET cc_start: 0.9023 (mtm) cc_final: 0.7858 (tpp) REVERT: A 808 LEU cc_start: 0.9270 (pp) cc_final: 0.8659 (tt) REVERT: A 809 VAL cc_start: 0.9340 (p) cc_final: 0.9051 (t) REVERT: B 573 ILE cc_start: 0.9417 (tp) cc_final: 0.9108 (tt) REVERT: B 788 SER cc_start: 0.8851 (p) cc_final: 0.8134 (m) REVERT: C 585 MET cc_start: 0.8590 (mmm) cc_final: 0.8099 (mmm) REVERT: C 590 ASP cc_start: 0.6038 (t0) cc_final: 0.5807 (t0) REVERT: C 650 LEU cc_start: 0.8202 (tp) cc_final: 0.7913 (tp) REVERT: C 670 MET cc_start: 0.9114 (mtt) cc_final: 0.8052 (mmp) REVERT: D 659 PHE cc_start: 0.7914 (m-80) cc_final: 0.7479 (m-80) REVERT: D 788 SER cc_start: 0.8717 (p) cc_final: 0.8497 (m) REVERT: D 813 GLU cc_start: 0.8224 (pp20) cc_final: 0.7983 (tm-30) REVERT: E 57 MET cc_start: 0.7209 (mpp) cc_final: 0.6688 (mpp) REVERT: E 181 PHE cc_start: 0.7388 (m-80) cc_final: 0.7188 (m-80) REVERT: E 199 MET cc_start: 0.8407 (tpt) cc_final: 0.8085 (tpp) REVERT: F 31 TYR cc_start: 0.7157 (m-10) cc_final: 0.6921 (m-80) REVERT: F 130 ARG cc_start: 0.5034 (mtt180) cc_final: 0.3923 (ttt90) REVERT: F 135 LEU cc_start: 0.8327 (mt) cc_final: 0.8100 (mt) REVERT: G 130 ARG cc_start: 0.5334 (mtt180) cc_final: 0.3871 (ttt90) REVERT: H 173 TYR cc_start: 0.8576 (p90) cc_final: 0.8357 (p90) REVERT: H 177 TRP cc_start: 0.7187 (p90) cc_final: 0.5376 (m100) REVERT: H 181 PHE cc_start: 0.7705 (m-10) cc_final: 0.7319 (m-10) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1269 time to fit residues: 62.0600 Evaluate side-chains 227 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 67 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.135342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.101801 restraints weight = 50059.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103769 restraints weight = 73510.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.104201 restraints weight = 46373.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.104254 restraints weight = 35104.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.104697 restraints weight = 32295.566| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18698 Z= 0.163 Angle : 0.642 9.986 25226 Z= 0.338 Chirality : 0.043 0.209 2826 Planarity : 0.004 0.052 3102 Dihedral : 4.813 78.243 2522 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.87 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2298 helix: 1.59 (0.15), residues: 1228 sheet: -1.30 (0.40), residues: 162 loop : -0.94 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 5 TYR 0.024 0.001 TYR C 523 PHE 0.027 0.002 PHE G 140 TRP 0.021 0.001 TRP E 177 HIS 0.009 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00358 (18686) covalent geometry : angle 0.64090 (25202) SS BOND : bond 0.00239 ( 12) SS BOND : angle 1.44582 ( 24) hydrogen bonds : bond 0.05136 ( 952) hydrogen bonds : angle 4.50011 ( 2724) *********************** 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 302 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.742 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 438 PHE cc_start: 0.7552 (p90) cc_final: 0.7348 (p90) REVERT: A 585 MET cc_start: 0.9034 (tpp) cc_final: 0.8753 (tpp) REVERT: A 670 MET cc_start: 0.8861 (mtm) cc_final: 0.7766 (mmt) REVERT: A 674 MET cc_start: 0.7721 (mmt) cc_final: 0.7499 (mmm) REVERT: A 809 VAL cc_start: 0.9308 (p) cc_final: 0.9104 (t) REVERT: B 463 MET cc_start: 0.5856 (mpp) cc_final: 0.4806 (mpp) REVERT: B 573 ILE cc_start: 0.9394 (tp) cc_final: 0.9080 (tt) REVERT: B 788 SER cc_start: 0.8833 (p) cc_final: 0.8080 (m) REVERT: C 585 MET cc_start: 0.8493 (mmm) cc_final: 0.7994 (mmm) REVERT: C 586 GLN cc_start: 0.7999 (pm20) cc_final: 0.7725 (pm20) REVERT: C 590 ASP cc_start: 0.5891 (t0) cc_final: 0.5579 (t0) REVERT: C 670 MET cc_start: 0.9077 (mtt) cc_final: 0.8137 (mmp) REVERT: C 721 MET cc_start: 0.8483 (ppp) cc_final: 0.8064 (ppp) REVERT: D 659 PHE cc_start: 0.7861 (m-80) cc_final: 0.7414 (m-80) REVERT: D 788 SER cc_start: 0.8770 (p) cc_final: 0.8546 (m) REVERT: E 181 PHE cc_start: 0.7335 (m-80) cc_final: 0.7097 (m-80) REVERT: E 199 MET cc_start: 0.8323 (tpt) cc_final: 0.7990 (tpp) REVERT: F 31 TYR cc_start: 0.7084 (m-10) cc_final: 0.6858 (m-80) REVERT: F 130 ARG cc_start: 0.5089 (mtt180) cc_final: 0.3987 (ttt90) REVERT: F 135 LEU cc_start: 0.8300 (mt) cc_final: 0.8053 (mt) REVERT: F 199 MET cc_start: 0.8487 (ttm) cc_final: 0.8272 (ttm) REVERT: G 130 ARG cc_start: 0.5275 (mtt180) cc_final: 0.3714 (ttt90) REVERT: H 177 TRP cc_start: 0.7140 (p90) cc_final: 0.5312 (m100) REVERT: H 181 PHE cc_start: 0.7645 (m-10) cc_final: 0.7245 (m-10) REVERT: H 199 MET cc_start: 0.8232 (tpp) cc_final: 0.7952 (tpp) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1256 time to fit residues: 60.8104 Evaluate side-chains 232 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 149 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** G 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 = 0.4010 r_free = 0.4010 target = 0.134864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.101769 restraints weight = 49987.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100159 restraints weight = 75779.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101178 restraints weight = 63238.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.101667 restraints weight = 42050.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101900 restraints weight = 37810.426| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18698 Z= 0.162 Angle : 0.639 8.850 25226 Z= 0.337 Chirality : 0.043 0.205 2826 Planarity : 0.004 0.051 3102 Dihedral : 4.798 79.914 2522 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.18 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.18), residues: 2298 helix: 1.45 (0.15), residues: 1242 sheet: -1.32 (0.40), residues: 163 loop : -1.06 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 5 TYR 0.022 0.001 TYR A 647 PHE 0.028 0.002 PHE G 140 TRP 0.028 0.001 TRP F 32 HIS 0.008 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00358 (18686) covalent geometry : angle 0.63760 (25202) SS BOND : bond 0.00242 ( 12) SS BOND : angle 1.36312 ( 24) hydrogen bonds : bond 0.05113 ( 952) hydrogen bonds : angle 4.52331 ( 2724) ********************** 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 302 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7681 (tpt) cc_final: 0.7471 (tpp) REVERT: A 408 MET cc_start: 0.6870 (tpt) cc_final: 0.6630 (tpt) REVERT: A 438 PHE cc_start: 0.7864 (p90) cc_final: 0.7496 (p90) REVERT: A 585 MET cc_start: 0.9111 (tpp) cc_final: 0.8888 (tpp) REVERT: A 670 MET cc_start: 0.8964 (mtm) cc_final: 0.8172 (mmt) REVERT: A 808 LEU cc_start: 0.9310 (pp) cc_final: 0.8703 (tt) REVERT: A 809 VAL cc_start: 0.9326 (p) cc_final: 0.9027 (t) REVERT: B 463 MET cc_start: 0.5893 (mpp) cc_final: 0.4960 (mpp) REVERT: B 788 SER cc_start: 0.8805 (p) cc_final: 0.8092 (m) REVERT: C 585 MET cc_start: 0.8446 (mmm) cc_final: 0.7911 (mmm) REVERT: C 586 GLN cc_start: 0.7959 (pm20) cc_final: 0.7542 (pm20) REVERT: C 670 MET cc_start: 0.9143 (mtt) cc_final: 0.8124 (mmp) REVERT: C 721 MET cc_start: 0.8568 (ppp) cc_final: 0.7963 (ppp) REVERT: D 503 MET cc_start: 0.7788 (ttm) cc_final: 0.7561 (ttp) REVERT: D 659 PHE cc_start: 0.7897 (m-80) cc_final: 0.7395 (m-80) REVERT: D 788 SER cc_start: 0.8659 (p) cc_final: 0.8444 (m) REVERT: E 199 MET cc_start: 0.8288 (tpt) cc_final: 0.8064 (tpp) REVERT: F 31 TYR cc_start: 0.7316 (m-10) cc_final: 0.7068 (m-80) REVERT: F 130 ARG cc_start: 0.5339 (mtt180) cc_final: 0.4190 (ttt90) REVERT: F 135 LEU cc_start: 0.8305 (mt) cc_final: 0.8000 (mt) REVERT: F 188 ILE cc_start: 0.8782 (mp) cc_final: 0.8443 (mp) REVERT: F 202 ASP cc_start: 0.8206 (t70) cc_final: 0.7675 (t70) REVERT: G 130 ARG cc_start: 0.5247 (mtt180) cc_final: 0.3608 (ttt90) REVERT: H 177 TRP cc_start: 0.7132 (p90) cc_final: 0.5262 (m100) REVERT: H 181 PHE cc_start: 0.7667 (m-10) cc_final: 0.7265 (m-10) REVERT: H 199 MET cc_start: 0.8272 (tpp) cc_final: 0.7951 (tpp) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1304 time to fit residues: 61.9690 Evaluate side-chains 229 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 172 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 228 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 176 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** 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 = 0.3987 r_free = 0.3987 target = 0.133187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099500 restraints weight = 48519.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100166 restraints weight = 78867.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100955 restraints weight = 52507.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.101290 restraints weight = 37564.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101956 restraints weight = 34090.754| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18698 Z= 0.183 Angle : 0.665 10.545 25226 Z= 0.351 Chirality : 0.044 0.204 2826 Planarity : 0.004 0.051 3102 Dihedral : 4.915 80.406 2522 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.18), residues: 2298 helix: 1.35 (0.15), residues: 1250 sheet: -1.43 (0.39), residues: 169 loop : -1.15 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 5 TYR 0.021 0.002 TYR C 732 PHE 0.019 0.002 PHE G 140 TRP 0.035 0.002 TRP F 32 HIS 0.008 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00406 (18686) covalent geometry : angle 0.66432 (25202) SS BOND : bond 0.00266 ( 12) SS BOND : angle 1.39795 ( 24) hydrogen bonds : bond 0.05404 ( 952) hydrogen bonds : angle 4.56458 ( 2724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2796.90 seconds wall clock time: 49 minutes 17.61 seconds (2957.61 seconds total)