Starting phenix.real_space_refine on Thu Sep 18 16:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrl_48558/09_2025/9mrl_48558.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrl_48558/09_2025/9mrl_48558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mrl_48558/09_2025/9mrl_48558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrl_48558/09_2025/9mrl_48558.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mrl_48558/09_2025/9mrl_48558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrl_48558/09_2025/9mrl_48558.map" } resolution = 4.17 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= 0.012 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 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: 4.14, per 1000 atoms: 0.23 Number of scatterers: 18294 At special positions: 0 Unit cell: (111.55, 132.89, 151.32, 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=2.04 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: 1.70 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 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: 99 helices and 23 sheets defined 58.5% alpha, 7.9% 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: 3.973A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.906A 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 521 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.597A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.883A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.699A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.745A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.752A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 4.108A 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 714 removed outlier: 4.242A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 removed outlier: 4.379A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 792 through 818 removed outlier: 4.256A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (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: 3.973A 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 521 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 522 through 546 removed outlier: 4.454A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.503A pdb=" N PHE B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.676A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.542A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.705A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.549A 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 696 Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.783A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.781A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 3.516A 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: 3.614A pdb=" N LYS B 776 " --> pdb=" O CYS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 817 removed outlier: 3.822A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.571A 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: 4.374A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 4.246A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 removed outlier: 3.712A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 3.775A 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: 3.892A 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: 3.622A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 786 removed outlier: 3.916A pdb=" N SER C 785 " --> pdb=" O GLU C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 818 removed outlier: 4.367A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.740A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 removed outlier: 4.041A 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 removed outlier: 3.559A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 521 through 545 removed outlier: 4.406A pdb=" N ILE D 525 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.595A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.735A 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: 3.654A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.778A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 749 " --> pdb=" O PRO D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 removed outlier: 4.295A 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: 4.217A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.722A pdb=" N LEU E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA E 16 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE E 17 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.732A 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: 3.681A pdb=" N ARG E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 124 removed outlier: 3.997A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 4.088A pdb=" N LEU E 135 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER E 136 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 4.008A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU E 207 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR E 208 " --> pdb=" O HIS E 204 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 28 Processing helix chain 'F' and resid 94 through 104 removed outlier: 4.468A pdb=" N ALA F 99 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 100 " --> pdb=" O PHE F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.587A pdb=" N ILE F 108 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 4.214A 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: 3.864A pdb=" N ALA F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 206 removed outlier: 3.886A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 3.719A 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: 4.698A pdb=" N ALA G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 123 removed outlier: 3.537A 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 160 removed outlier: 3.906A pdb=" N LEU G 135 " --> pdb=" O HIS G 131 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE G 149 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 206 removed outlier: 3.870A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.651A pdb=" N LEU H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY H 15 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA H 16 " --> pdb=" O THR H 12 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE H 17 " --> pdb=" O THR H 13 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA H 18 " --> pdb=" O VAL H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 removed outlier: 3.755A 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: 3.708A pdb=" N ARG H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.976A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 160 removed outlier: 3.879A pdb=" N LEU H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 206 removed outlier: 4.076A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.511A 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 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.211A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 3.506A pdb=" N LEU A 703 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.929A 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 490 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.625A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.560A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.259A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.581A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 439 through 444 removed outlier: 6.907A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.742A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.110A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC3, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.796A pdb=" N LEU F 33 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.598A pdb=" N LEU G 33 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER G 174 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 76 through 78 969 hydrogen bonds defined for protein. 2775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 2.15 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: 5609 1.34 - 1.46: 4561 1.46 - 1.58: 8308 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 18686 Sorted by residual: bond pdb=" CG1 ILE F 188 " pdb=" CD1 ILE F 188 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CE1 TYR D 616 " pdb=" CZ TYR D 616 " ideal model delta sigma weight residual 1.378 1.351 0.027 2.40e-02 1.74e+03 1.28e+00 bond pdb=" CB ASN A 619 " pdb=" CG ASN A 619 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" CB THR A 609 " pdb=" CG2 THR A 609 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CE1 TYR B 616 " pdb=" CZ TYR B 616 " ideal model delta sigma weight residual 1.378 1.352 0.026 2.40e-02 1.74e+03 1.18e+00 ... (remaining 18681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 24391 1.68 - 3.37: 716 3.37 - 5.05: 79 5.05 - 6.74: 14 6.74 - 8.42: 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 121.97 130.39 -8.42 1.80e+00 3.09e-01 2.19e+01 angle pdb=" N THR B 457 " pdb=" CA THR B 457 " pdb=" C THR B 457 " ideal model delta sigma weight residual 114.56 109.87 4.69 1.27e+00 6.20e-01 1.36e+01 angle pdb=" N ASP C 519 " pdb=" CA ASP C 519 " pdb=" C ASP C 519 " ideal model delta sigma weight residual 109.81 117.37 -7.56 2.21e+00 2.05e-01 1.17e+01 angle pdb=" CA TYR A 732 " pdb=" CB TYR A 732 " pdb=" CG TYR A 732 " ideal model delta sigma weight residual 113.90 119.91 -6.01 1.80e+00 3.09e-01 1.11e+01 angle pdb=" C GLY B 725 " pdb=" N ASN B 726 " pdb=" CA ASN B 726 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.73e+00 ... (remaining 25197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10260 17.71 - 35.41: 595 35.41 - 53.12: 87 53.12 - 70.83: 22 70.83 - 88.54: 12 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 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+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 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA SER A 785 " pdb=" C SER A 785 " pdb=" N ALA A 786 " pdb=" CA ALA A 786 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 10973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1968 0.043 - 0.087: 655 0.087 - 0.130: 171 0.130 - 0.174: 24 0.174 - 0.217: 8 Chirality restraints: 2826 Sorted by residual: 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 2.31 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PRO D 520 " pdb=" N PRO D 520 " pdb=" C PRO D 520 " pdb=" CB PRO D 520 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PRO B 520 " pdb=" N PRO B 520 " pdb=" C PRO B 520 " pdb=" CB PRO B 520 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2823 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO D 520 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 520 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 605 " 0.009 2.00e-02 2.50e+03 1.35e-02 4.57e+00 pdb=" CG TRP D 605 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 605 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 605 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 605 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 605 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 605 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 605 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 605 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 605 " 0.002 2.00e-02 2.50e+03 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 388 2.69 - 3.24: 19670 3.24 - 3.80: 27637 3.80 - 4.35: 34042 4.35 - 4.90: 57133 Nonbonded interactions: 138870 Sorted by model distance: nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.140 3.040 nonbonded pdb=" O LYS A 409 " pdb=" ND1 HIS A 412 " model vdw 2.203 3.120 nonbonded pdb=" OD2 ASP B 454 " pdb=" OG1 THR B 457 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 655 " pdb=" OE2 GLU A1301 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU B 657 " pdb=" NH1 ARG B 660 " model vdw 2.234 3.120 ... (remaining 138865 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: 7.790 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.900 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 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 : 0.004 0.054 18698 Z= 0.190 Angle : 0.675 8.424 25226 Z= 0.382 Chirality : 0.046 0.217 2826 Planarity : 0.006 0.066 3102 Dihedral : 12.021 88.536 6664 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.13 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: -0.71 (0.16), residues: 2298 helix: 0.12 (0.14), residues: 1203 sheet: -1.14 (0.42), residues: 139 loop : -1.00 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 545 TYR 0.025 0.002 TYR A 732 PHE 0.021 0.002 PHE A 659 TRP 0.036 0.003 TRP A 605 HIS 0.004 0.001 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00427 (18686) covalent geometry : angle 0.67512 (25202) SS BOND : bond 0.00223 ( 12) SS BOND : angle 0.74161 ( 24) hydrogen bonds : bond 0.16844 ( 969) hydrogen bonds : angle 6.23321 ( 2775) *********************** 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 486 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ILE cc_start: 0.7869 (mm) cc_final: 0.7172 (tt) REVERT: A 523 TYR cc_start: 0.7128 (t80) cc_final: 0.6602 (t80) REVERT: A 785 SER cc_start: 0.7346 (m) cc_final: 0.7092 (t) REVERT: B 519 ASP cc_start: 0.8522 (m-30) cc_final: 0.8305 (m-30) REVERT: B 704 LEU cc_start: 0.9205 (pt) cc_final: 0.8890 (pt) REVERT: B 790 SER cc_start: 0.8855 (m) cc_final: 0.8479 (t) REVERT: C 586 GLN cc_start: 0.8743 (mt0) cc_final: 0.8381 (tp40) REVERT: C 721 MET cc_start: 0.6606 (ptt) cc_final: 0.6273 (ptt) REVERT: D 631 SER cc_start: 0.8238 (m) cc_final: 0.8034 (p) REVERT: D 704 LEU cc_start: 0.8800 (pt) cc_final: 0.8512 (pt) REVERT: D 708 MET cc_start: 0.7847 (mtm) cc_final: 0.7631 (mtm) REVERT: D 790 SER cc_start: 0.8711 (m) cc_final: 0.8390 (t) REVERT: F 159 ASN cc_start: 0.7314 (m-40) cc_final: 0.6559 (t0) REVERT: F 184 LEU cc_start: 0.8266 (tp) cc_final: 0.7999 (tp) REVERT: G 173 TYR cc_start: 0.6542 (p90) cc_final: 0.6162 (p90) REVERT: G 175 TYR cc_start: 0.4841 (m-80) cc_final: 0.4619 (m-80) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.1494 time to fit residues: 106.2120 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 : 0.745 ------------------------------------------------------------------------------- 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: 0.7980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN H 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.172993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152195 restraints weight = 37046.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.150483 restraints weight = 78989.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.148952 restraints weight = 45916.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149227 restraints weight = 42704.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.149676 restraints weight = 30330.229| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2714 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= 0.138 Angle : 0.592 7.550 25226 Z= 0.323 Chirality : 0.043 0.177 2826 Planarity : 0.004 0.047 3102 Dihedral : 5.234 67.905 2522 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.05 % Favored : 96.74 % Rotamer: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.18), residues: 2298 helix: 1.67 (0.15), residues: 1213 sheet: -0.79 (0.42), residues: 138 loop : -0.80 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 98 TYR 0.017 0.001 TYR C 533 PHE 0.018 0.002 PHE F 17 TRP 0.019 0.001 TRP D 460 HIS 0.012 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00287 (18686) covalent geometry : angle 0.59202 (25202) SS BOND : bond 0.00152 ( 12) SS BOND : angle 0.54043 ( 24) hydrogen bonds : bond 0.05270 ( 969) hydrogen bonds : angle 4.57417 ( 2775) *********************** 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 328 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.604 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 444 ILE cc_start: 0.7803 (mm) cc_final: 0.7119 (tt) REVERT: A 536 VAL cc_start: 0.9037 (p) cc_final: 0.8769 (t) REVERT: A 604 VAL cc_start: 0.9237 (t) cc_final: 0.9014 (m) REVERT: A 785 SER cc_start: 0.6871 (m) cc_final: 0.6509 (t) REVERT: B 708 MET cc_start: 0.7039 (mtm) cc_final: 0.6388 (mtm) REVERT: B 788 SER cc_start: 0.8508 (p) cc_final: 0.8122 (m) REVERT: B 790 SER cc_start: 0.8761 (m) cc_final: 0.8153 (t) REVERT: C 790 SER cc_start: 0.8535 (p) cc_final: 0.8012 (t) REVERT: D 496 MET cc_start: 0.7069 (ppp) cc_final: 0.6625 (ppp) REVERT: D 711 TYR cc_start: 0.6819 (t80) cc_final: 0.6312 (t80) REVERT: D 790 SER cc_start: 0.8591 (m) cc_final: 0.8181 (t) REVERT: F 184 LEU cc_start: 0.8446 (tp) cc_final: 0.8167 (tp) REVERT: H 194 VAL cc_start: 0.7857 (t) cc_final: 0.7503 (t) outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.1155 time to fit residues: 58.9435 Evaluate side-chains 215 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.164562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143169 restraints weight = 38319.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137585 restraints weight = 59822.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.135920 restraints weight = 52802.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134919 restraints weight = 54665.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.133831 restraints weight = 47435.928| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 18698 Z= 0.307 Angle : 0.764 9.868 25226 Z= 0.417 Chirality : 0.049 0.230 2826 Planarity : 0.005 0.078 3102 Dihedral : 5.817 81.577 2522 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % 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: 0.14 (0.17), residues: 2298 helix: 1.19 (0.15), residues: 1200 sheet: -1.21 (0.38), residues: 147 loop : -1.10 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 684 TYR 0.030 0.002 TYR A 616 PHE 0.036 0.003 PHE C 515 TRP 0.038 0.003 TRP C 460 HIS 0.009 0.001 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00706 (18686) covalent geometry : angle 0.76413 (25202) SS BOND : bond 0.00589 ( 12) SS BOND : angle 0.79273 ( 24) hydrogen bonds : bond 0.07255 ( 969) hydrogen bonds : angle 5.13583 ( 2775) *********************** 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 265 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ILE cc_start: 0.8474 (mm) cc_final: 0.7841 (tt) REVERT: A 503 MET cc_start: 0.8652 (ttp) cc_final: 0.8355 (ttt) REVERT: A 536 VAL cc_start: 0.9094 (p) cc_final: 0.8793 (t) REVERT: A 790 SER cc_start: 0.8974 (p) cc_final: 0.8753 (t) REVERT: B 408 MET cc_start: 0.5395 (tmm) cc_final: 0.5188 (ptp) REVERT: B 790 SER cc_start: 0.8982 (m) cc_final: 0.8597 (t) REVERT: C 463 MET cc_start: 0.8354 (ttp) cc_final: 0.8038 (ttp) REVERT: C 523 TYR cc_start: 0.6112 (t80) cc_final: 0.5820 (t80) REVERT: C 536 VAL cc_start: 0.9100 (p) cc_final: 0.8762 (t) REVERT: C 700 TYR cc_start: 0.6339 (t80) cc_final: 0.6052 (t80) REVERT: C 790 SER cc_start: 0.8811 (p) cc_final: 0.8246 (t) REVERT: D 503 MET cc_start: 0.8436 (mtt) cc_final: 0.8128 (mtt) REVERT: D 711 TYR cc_start: 0.7130 (t80) cc_final: 0.6571 (t80) REVERT: D 790 SER cc_start: 0.8635 (m) cc_final: 0.8318 (t) REVERT: E 23 MET cc_start: 0.7878 (ptt) cc_final: 0.7464 (ptt) REVERT: H 194 VAL cc_start: 0.8114 (t) cc_final: 0.7627 (t) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1244 time to fit residues: 51.4151 Evaluate side-chains 202 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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: 3.9990 chunk 201 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 123 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 159 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 HIS ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.160971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140075 restraints weight = 37963.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.133807 restraints weight = 58530.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.130833 restraints weight = 58200.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130129 restraints weight = 56414.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128822 restraints weight = 49604.158| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 18698 Z= 0.376 Angle : 0.843 10.549 25226 Z= 0.459 Chirality : 0.051 0.231 2826 Planarity : 0.006 0.086 3102 Dihedral : 6.178 80.993 2522 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.44 % Favored : 95.34 % Rotamer: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.12 % 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: -0.65 (0.17), residues: 2298 helix: 0.66 (0.14), residues: 1214 sheet: -1.57 (0.40), residues: 127 loop : -1.69 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 660 TYR 0.035 0.003 TYR A 616 PHE 0.052 0.003 PHE C 515 TRP 0.044 0.003 TRP C 460 HIS 0.010 0.002 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00867 (18686) covalent geometry : angle 0.84338 (25202) SS BOND : bond 0.00243 ( 12) SS BOND : angle 0.91775 ( 24) hydrogen bonds : bond 0.07648 ( 969) hydrogen bonds : angle 5.49009 ( 2775) *********************** 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 254 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.8536 (ttp) cc_final: 0.8284 (ttt) REVERT: A 599 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8234 (mtp85) REVERT: A 790 SER cc_start: 0.9074 (p) cc_final: 0.8848 (t) REVERT: B 408 MET cc_start: 0.6388 (tmm) cc_final: 0.5774 (ppp) REVERT: B 790 SER cc_start: 0.9139 (m) cc_final: 0.8671 (t) REVERT: C 463 MET cc_start: 0.8443 (ttp) cc_final: 0.8036 (ttp) REVERT: C 585 MET cc_start: 0.8669 (mmm) cc_final: 0.8460 (mmm) REVERT: C 599 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8313 (mtp85) REVERT: C 788 SER cc_start: 0.8918 (t) cc_final: 0.8624 (p) REVERT: D 711 TYR cc_start: 0.7350 (t80) cc_final: 0.6970 (t80) REVERT: D 790 SER cc_start: 0.8715 (m) cc_final: 0.8328 (t) REVERT: E 194 VAL cc_start: 0.8118 (t) cc_final: 0.7787 (t) REVERT: G 159 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.6483 (t0) REVERT: G 199 MET cc_start: 0.6998 (mmt) cc_final: 0.6435 (mtp) REVERT: H 194 VAL cc_start: 0.8134 (t) cc_final: 0.7642 (t) outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.1219 time to fit residues: 48.8177 Evaluate side-chains 204 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 0.6980 chunk 59 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 212 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN D 714 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 HIS G 148 ASN G 159 ASN G 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.167559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.146341 restraints weight = 38071.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.141276 restraints weight = 52878.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.136037 restraints weight = 69045.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.136397 restraints weight = 62960.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.136434 restraints weight = 45751.954| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4647 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= 0.127 Angle : 0.574 8.036 25226 Z= 0.311 Chirality : 0.042 0.178 2826 Planarity : 0.004 0.062 3102 Dihedral : 5.095 71.791 2522 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.83 % Favored : 96.95 % Rotamer: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.18), residues: 2298 helix: 1.48 (0.15), residues: 1222 sheet: -1.48 (0.38), residues: 146 loop : -1.21 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 36 TYR 0.016 0.001 TYR A 732 PHE 0.018 0.001 PHE E 140 TRP 0.013 0.001 TRP B 526 HIS 0.003 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00268 (18686) covalent geometry : angle 0.57407 (25202) SS BOND : bond 0.00213 ( 12) SS BOND : angle 0.77106 ( 24) hydrogen bonds : bond 0.05141 ( 969) hydrogen bonds : angle 4.37116 ( 2775) *********************** 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 269 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.699 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 750 VAL cc_start: 0.8578 (p) cc_final: 0.8280 (t) REVERT: A 790 SER cc_start: 0.8694 (p) cc_final: 0.8287 (t) REVERT: B 408 MET cc_start: 0.6137 (tmm) cc_final: 0.5368 (ppp) REVERT: B 790 SER cc_start: 0.8957 (m) cc_final: 0.8500 (t) REVERT: C 503 MET cc_start: 0.8263 (ttp) cc_final: 0.8061 (ttt) REVERT: C 533 TYR cc_start: 0.8534 (t80) cc_final: 0.8310 (t80) REVERT: C 585 MET cc_start: 0.8235 (mmm) cc_final: 0.7827 (mmm) REVERT: C 670 MET cc_start: 0.7680 (mtp) cc_final: 0.7400 (mtm) REVERT: C 700 TYR cc_start: 0.6672 (t80) cc_final: 0.6406 (t80) REVERT: C 750 VAL cc_start: 0.8584 (p) cc_final: 0.8314 (t) REVERT: C 788 SER cc_start: 0.8797 (t) cc_final: 0.8524 (p) REVERT: D 533 TYR cc_start: 0.7799 (t80) cc_final: 0.7536 (t80) REVERT: D 585 MET cc_start: 0.7634 (mmm) cc_final: 0.7201 (mmm) REVERT: D 671 TRP cc_start: 0.6105 (t-100) cc_final: 0.5873 (t-100) REVERT: D 711 TYR cc_start: 0.7126 (t80) cc_final: 0.6785 (t80) REVERT: D 790 SER cc_start: 0.8618 (m) cc_final: 0.8183 (t) REVERT: E 194 VAL cc_start: 0.7808 (t) cc_final: 0.7567 (t) REVERT: F 159 ASN cc_start: 0.7582 (m-40) cc_final: 0.6799 (t0) REVERT: G 159 ASN cc_start: 0.7485 (m-40) cc_final: 0.6646 (t0) REVERT: H 194 VAL cc_start: 0.8139 (t) cc_final: 0.7738 (t) outliers start: 1 outliers final: 0 residues processed: 268 average time/residue: 0.1235 time to fit residues: 51.8652 Evaluate side-chains 208 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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: 0.9980 chunk 179 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 2 optimal weight: 0.0070 chunk 224 optimal weight: 0.3980 chunk 216 optimal weight: 0.0270 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 HIS G 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.169187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148353 restraints weight = 37554.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.144278 restraints weight = 52217.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.139848 restraints weight = 54540.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139069 restraints weight = 55063.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137296 restraints weight = 52467.671| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18698 Z= 0.113 Angle : 0.544 7.449 25226 Z= 0.292 Chirality : 0.041 0.178 2826 Planarity : 0.004 0.057 3102 Dihedral : 4.707 72.190 2522 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.39 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 0.61 (0.18), residues: 2298 helix: 1.72 (0.15), residues: 1227 sheet: -1.23 (0.37), residues: 158 loop : -1.13 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 36 TYR 0.014 0.001 TYR A 732 PHE 0.022 0.001 PHE B 541 TRP 0.017 0.001 TRP C 767 HIS 0.002 0.001 HIS E 59 Details of bonding type rmsd covalent geometry : bond 0.00234 (18686) covalent geometry : angle 0.54350 (25202) SS BOND : bond 0.00174 ( 12) SS BOND : angle 0.65804 ( 24) hydrogen bonds : bond 0.04477 ( 969) hydrogen bonds : angle 4.18114 ( 2775) *********************** 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 260 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.747 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 750 VAL cc_start: 0.8559 (p) cc_final: 0.8275 (t) REVERT: A 790 SER cc_start: 0.8728 (p) cc_final: 0.8233 (t) REVERT: B 408 MET cc_start: 0.5826 (tmm) cc_final: 0.5156 (ppp) REVERT: B 790 SER cc_start: 0.8923 (m) cc_final: 0.8405 (t) REVERT: C 421 TYR cc_start: 0.7503 (m-80) cc_final: 0.6979 (m-80) REVERT: C 585 MET cc_start: 0.8035 (mmm) cc_final: 0.7613 (mmm) REVERT: C 670 MET cc_start: 0.7676 (mtp) cc_final: 0.7442 (mtm) REVERT: C 700 TYR cc_start: 0.6676 (t80) cc_final: 0.6275 (t80) REVERT: C 788 SER cc_start: 0.8808 (t) cc_final: 0.8539 (p) REVERT: D 629 MET cc_start: 0.7758 (mmm) cc_final: 0.7015 (mmm) REVERT: D 711 TYR cc_start: 0.7178 (t80) cc_final: 0.6851 (t80) REVERT: D 790 SER cc_start: 0.8534 (m) cc_final: 0.8151 (t) REVERT: E 194 VAL cc_start: 0.7812 (t) cc_final: 0.7559 (t) REVERT: F 159 ASN cc_start: 0.7731 (m-40) cc_final: 0.6876 (t0) REVERT: F 184 LEU cc_start: 0.8460 (tp) cc_final: 0.8067 (tp) REVERT: G 159 ASN cc_start: 0.7618 (m-40) cc_final: 0.6685 (t0) REVERT: H 194 VAL cc_start: 0.8104 (t) cc_final: 0.7766 (t) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1291 time to fit residues: 52.8801 Evaluate side-chains 202 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 0.9980 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 193 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 HIS G 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.167184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145394 restraints weight = 37267.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140732 restraints weight = 59907.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137665 restraints weight = 52217.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.137063 restraints weight = 54641.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.136081 restraints weight = 45158.269| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.5022 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= 0.145 Angle : 0.573 8.620 25226 Z= 0.309 Chirality : 0.042 0.187 2826 Planarity : 0.004 0.059 3102 Dihedral : 4.753 70.066 2522 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.35 % Favored : 96.34 % 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: 0.59 (0.18), residues: 2298 helix: 1.73 (0.15), residues: 1222 sheet: -1.19 (0.38), residues: 154 loop : -1.18 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 36 TYR 0.030 0.001 TYR B 673 PHE 0.031 0.001 PHE E 140 TRP 0.013 0.001 TRP C 460 HIS 0.004 0.001 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00329 (18686) covalent geometry : angle 0.57313 (25202) SS BOND : bond 0.00124 ( 12) SS BOND : angle 0.59669 ( 24) hydrogen bonds : bond 0.05089 ( 969) hydrogen bonds : angle 4.30954 ( 2775) *********************** 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 254 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ILE cc_start: 0.8690 (mm) cc_final: 0.8447 (mt) REVERT: A 536 VAL cc_start: 0.9099 (p) cc_final: 0.8809 (t) REVERT: A 750 VAL cc_start: 0.8615 (p) cc_final: 0.8310 (t) REVERT: A 790 SER cc_start: 0.8768 (p) cc_final: 0.8350 (t) REVERT: B 408 MET cc_start: 0.5930 (tmm) cc_final: 0.5244 (ppp) REVERT: B 585 MET cc_start: 0.7504 (mtm) cc_final: 0.7180 (mtt) REVERT: B 790 SER cc_start: 0.8918 (m) cc_final: 0.8368 (t) REVERT: C 585 MET cc_start: 0.8272 (mmm) cc_final: 0.7936 (mmm) REVERT: C 670 MET cc_start: 0.7562 (mtp) cc_final: 0.7337 (mtm) REVERT: C 788 SER cc_start: 0.8863 (t) cc_final: 0.8542 (p) REVERT: D 629 MET cc_start: 0.7793 (mmm) cc_final: 0.7065 (mmm) REVERT: D 711 TYR cc_start: 0.7249 (t80) cc_final: 0.6908 (t80) REVERT: D 790 SER cc_start: 0.8565 (m) cc_final: 0.8138 (t) REVERT: E 159 ASN cc_start: 0.8007 (m110) cc_final: 0.7764 (m110) REVERT: F 159 ASN cc_start: 0.7834 (m-40) cc_final: 0.6910 (t0) REVERT: G 159 ASN cc_start: 0.7691 (m-40) cc_final: 0.6744 (t0) REVERT: H 194 VAL cc_start: 0.8076 (t) cc_final: 0.7691 (t) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1345 time to fit residues: 53.6181 Evaluate side-chains 207 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 83 optimal weight: 0.0010 chunk 69 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** 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 = 0.4191 r_free = 0.4191 target = 0.162376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141313 restraints weight = 38207.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.136375 restraints weight = 56938.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.132696 restraints weight = 57747.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.132009 restraints weight = 56526.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.131046 restraints weight = 47764.178| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 18698 Z= 0.286 Angle : 0.739 8.836 25226 Z= 0.401 Chirality : 0.047 0.203 2826 Planarity : 0.005 0.069 3102 Dihedral : 5.499 75.057 2522 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.00 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -0.22 (0.17), residues: 2298 helix: 1.08 (0.15), residues: 1228 sheet: -1.28 (0.36), residues: 173 loop : -1.65 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 98 TYR 0.020 0.002 TYR A 616 PHE 0.034 0.002 PHE C 515 TRP 0.034 0.003 TRP C 460 HIS 0.007 0.001 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00662 (18686) covalent geometry : angle 0.73859 (25202) SS BOND : bond 0.00160 ( 12) SS BOND : angle 0.73471 ( 24) hydrogen bonds : bond 0.06919 ( 969) hydrogen bonds : angle 5.03832 ( 2775) *********************** 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 245 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 VAL cc_start: 0.9093 (p) cc_final: 0.8821 (t) REVERT: A 750 VAL cc_start: 0.8801 (p) cc_final: 0.8490 (t) REVERT: A 790 SER cc_start: 0.9107 (p) cc_final: 0.8904 (t) REVERT: B 408 MET cc_start: 0.6344 (tmm) cc_final: 0.5909 (ppp) REVERT: B 790 SER cc_start: 0.8910 (m) cc_final: 0.8407 (t) REVERT: C 536 VAL cc_start: 0.9071 (p) cc_final: 0.8741 (t) REVERT: C 599 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.8070 (mtp85) REVERT: C 750 VAL cc_start: 0.8738 (p) cc_final: 0.8421 (t) REVERT: C 788 SER cc_start: 0.8930 (t) cc_final: 0.8676 (p) REVERT: D 790 SER cc_start: 0.8643 (m) cc_final: 0.8184 (t) REVERT: E 173 TYR cc_start: 0.7028 (p90) cc_final: 0.6717 (p90) REVERT: F 135 LEU cc_start: 0.3665 (tt) cc_final: 0.3176 (tp) REVERT: F 159 ASN cc_start: 0.7942 (m-40) cc_final: 0.6809 (t0) REVERT: F 199 MET cc_start: 0.5344 (mmm) cc_final: 0.5102 (mmm) REVERT: G 159 ASN cc_start: 0.7821 (m-40) cc_final: 0.6644 (t0) REVERT: H 116 MET cc_start: 0.7738 (pmm) cc_final: 0.6085 (tpt) REVERT: H 194 VAL cc_start: 0.8176 (t) cc_final: 0.7739 (t) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1380 time to fit residues: 53.0111 Evaluate side-chains 203 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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: 0.7980 chunk 226 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 169 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** G 59 HIS ** 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 = 0.4240 r_free = 0.4240 target = 0.166398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.144407 restraints weight = 38054.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.139796 restraints weight = 59263.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.136805 restraints weight = 53883.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.136544 restraints weight = 53849.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135631 restraints weight = 44476.949| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.5385 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= 0.135 Angle : 0.587 8.215 25226 Z= 0.316 Chirality : 0.042 0.179 2826 Planarity : 0.004 0.062 3102 Dihedral : 4.977 66.244 2522 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.00 % Favored : 96.74 % 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: 0.21 (0.18), residues: 2298 helix: 1.43 (0.15), residues: 1247 sheet: -1.37 (0.41), residues: 140 loop : -1.47 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 36 TYR 0.018 0.001 TYR B 533 PHE 0.027 0.001 PHE E 140 TRP 0.014 0.001 TRP B 526 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00298 (18686) covalent geometry : angle 0.58685 (25202) SS BOND : bond 0.00168 ( 12) SS BOND : angle 0.67776 ( 24) hydrogen bonds : bond 0.05350 ( 969) hydrogen bonds : angle 4.45912 ( 2775) *********************** 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 261 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ILE cc_start: 0.8798 (mm) cc_final: 0.8580 (mt) REVERT: A 533 TYR cc_start: 0.8698 (t80) cc_final: 0.8495 (t80) REVERT: A 536 VAL cc_start: 0.9151 (p) cc_final: 0.8875 (t) REVERT: A 750 VAL cc_start: 0.8720 (p) cc_final: 0.8393 (t) REVERT: A 790 SER cc_start: 0.8865 (p) cc_final: 0.8491 (t) REVERT: B 408 MET cc_start: 0.6235 (tmm) cc_final: 0.5575 (ppp) REVERT: B 790 SER cc_start: 0.8900 (m) cc_final: 0.8303 (t) REVERT: C 408 MET cc_start: 0.6933 (mmm) cc_final: 0.6701 (tpp) REVERT: C 421 TYR cc_start: 0.7607 (m-80) cc_final: 0.7074 (m-80) REVERT: C 670 MET cc_start: 0.7473 (mtp) cc_final: 0.7179 (mtm) REVERT: C 790 SER cc_start: 0.8736 (p) cc_final: 0.8481 (t) REVERT: D 407 MET cc_start: 0.5864 (pmm) cc_final: 0.5418 (pmm) REVERT: D 629 MET cc_start: 0.7781 (mmm) cc_final: 0.7522 (mmm) REVERT: D 671 TRP cc_start: 0.5945 (t-100) cc_final: 0.5411 (t-100) REVERT: D 790 SER cc_start: 0.8623 (m) cc_final: 0.8173 (t) REVERT: F 135 LEU cc_start: 0.3714 (tt) cc_final: 0.3239 (tp) REVERT: F 159 ASN cc_start: 0.7785 (m-40) cc_final: 0.6819 (t0) REVERT: F 199 MET cc_start: 0.5263 (mmm) cc_final: 0.4986 (mmm) REVERT: G 159 ASN cc_start: 0.7755 (m-40) cc_final: 0.6654 (t0) REVERT: H 194 VAL cc_start: 0.8156 (t) cc_final: 0.7839 (t) REVERT: H 199 MET cc_start: 0.8127 (ppp) cc_final: 0.7909 (ppp) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1312 time to fit residues: 53.5522 Evaluate side-chains 210 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 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: 0.9980 chunk 9 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 98 optimal weight: 0.0060 chunk 26 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** G 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 = 0.4263 r_free = 0.4263 target = 0.168333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.147585 restraints weight = 38612.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143499 restraints weight = 53386.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140775 restraints weight = 59049.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.140294 restraints weight = 61896.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139449 restraints weight = 44883.790| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18698 Z= 0.119 Angle : 0.581 11.691 25226 Z= 0.308 Chirality : 0.042 0.179 2826 Planarity : 0.004 0.054 3102 Dihedral : 4.643 64.790 2522 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.31 % Favored : 96.48 % 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: 0.37 (0.18), residues: 2298 helix: 1.56 (0.15), residues: 1256 sheet: -1.28 (0.37), residues: 158 loop : -1.43 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 715 TYR 0.032 0.001 TYR D 711 PHE 0.020 0.001 PHE E 140 TRP 0.009 0.001 TRP B 526 HIS 0.002 0.001 HIS E 59 Details of bonding type rmsd covalent geometry : bond 0.00247 (18686) covalent geometry : angle 0.58136 (25202) SS BOND : bond 0.00166 ( 12) SS BOND : angle 0.65349 ( 24) hydrogen bonds : bond 0.04536 ( 969) hydrogen bonds : angle 4.26877 ( 2775) ********************** 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 253 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ILE cc_start: 0.8776 (mm) cc_final: 0.8565 (mt) REVERT: A 536 VAL cc_start: 0.9106 (p) cc_final: 0.8787 (t) REVERT: A 750 VAL cc_start: 0.8556 (p) cc_final: 0.8265 (t) REVERT: B 408 MET cc_start: 0.6187 (tmm) cc_final: 0.5456 (ppp) REVERT: B 645 ILE cc_start: 0.6972 (mm) cc_final: 0.6755 (mm) REVERT: B 709 ASN cc_start: 0.8887 (t0) cc_final: 0.8588 (t0) REVERT: B 790 SER cc_start: 0.8907 (m) cc_final: 0.8309 (t) REVERT: C 670 MET cc_start: 0.7431 (mtp) cc_final: 0.7200 (mtm) REVERT: C 700 TYR cc_start: 0.6689 (t80) cc_final: 0.6226 (t80) REVERT: C 790 SER cc_start: 0.8734 (p) cc_final: 0.8404 (t) REVERT: D 407 MET cc_start: 0.5746 (pmm) cc_final: 0.5270 (pmm) REVERT: D 671 TRP cc_start: 0.5941 (t-100) cc_final: 0.5417 (t-100) REVERT: D 790 SER cc_start: 0.8563 (m) cc_final: 0.8083 (t) REVERT: E 23 MET cc_start: 0.7966 (ptt) cc_final: 0.7669 (ptt) REVERT: E 116 MET cc_start: 0.7447 (pmm) cc_final: 0.6079 (tpt) REVERT: E 194 VAL cc_start: 0.7804 (t) cc_final: 0.7371 (t) REVERT: F 135 LEU cc_start: 0.3724 (tt) cc_final: 0.3266 (tp) REVERT: F 159 ASN cc_start: 0.7930 (m-40) cc_final: 0.6911 (t0) REVERT: F 184 LEU cc_start: 0.8284 (tp) cc_final: 0.8020 (tp) REVERT: F 199 MET cc_start: 0.5082 (mmm) cc_final: 0.4829 (mmm) REVERT: G 148 ASN cc_start: 0.6950 (t0) cc_final: 0.6672 (t0) REVERT: G 159 ASN cc_start: 0.7637 (m-40) cc_final: 0.6637 (t0) REVERT: H 116 MET cc_start: 0.7695 (pmm) cc_final: 0.6080 (tpt) REVERT: H 194 VAL cc_start: 0.8030 (t) cc_final: 0.7707 (t) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1298 time to fit residues: 51.8689 Evaluate side-chains 204 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 176 optimal weight: 0.5980 chunk 170 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** 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 = 0.4214 r_free = 0.4214 target = 0.163553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.142801 restraints weight = 38504.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136934 restraints weight = 64220.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134879 restraints weight = 59188.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.134719 restraints weight = 55471.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133995 restraints weight = 46699.399| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18698 Z= 0.246 Angle : 0.696 12.046 25226 Z= 0.374 Chirality : 0.045 0.185 2826 Planarity : 0.005 0.065 3102 Dihedral : 5.189 76.283 2522 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.92 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.05 (0.17), residues: 2298 helix: 1.34 (0.15), residues: 1231 sheet: -1.38 (0.40), residues: 145 loop : -1.56 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 36 TYR 0.033 0.002 TYR D 711 PHE 0.029 0.002 PHE C 515 TRP 0.026 0.002 TRP C 460 HIS 0.007 0.001 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00571 (18686) covalent geometry : angle 0.69633 (25202) SS BOND : bond 0.00114 ( 12) SS BOND : angle 0.65772 ( 24) hydrogen bonds : bond 0.06298 ( 969) hydrogen bonds : angle 4.85832 ( 2775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.33 seconds wall clock time: 45 minutes 12.34 seconds (2712.34 seconds total)