Starting phenix.real_space_refine on Sat Mar 16 16:28:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwo_35775/03_2024/8iwo_35775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwo_35775/03_2024/8iwo_35775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwo_35775/03_2024/8iwo_35775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwo_35775/03_2024/8iwo_35775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwo_35775/03_2024/8iwo_35775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwo_35775/03_2024/8iwo_35775_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.104 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 9826 2.51 5 N 2516 2.21 5 O 2704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 803": "OD1" <-> "OD2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A ASP 827": "OD1" <-> "OD2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A GLU 939": "OE1" <-> "OE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 803": "OD1" <-> "OD2" Residue "B GLU 818": "OE1" <-> "OE2" Residue "B ASP 827": "OD1" <-> "OD2" Residue "B GLU 876": "OE1" <-> "OE2" Residue "B GLU 877": "OE1" <-> "OE2" Residue "B GLU 881": "OE1" <-> "OE2" Residue "B GLU 939": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7516 Classifications: {'peptide': 956} Link IDs: {'PTRANS': 32, 'TRANS': 923} Chain breaks: 3 Chain: "B" Number of atoms: 7516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7516 Classifications: {'peptide': 956} Link IDs: {'PTRANS': 32, 'TRANS': 923} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.56, per 1000 atoms: 0.57 Number of scatterers: 15118 At special positions: 0 Unit cell: (107.06, 100.7, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 2 15.00 O 2704 8.00 N 2516 7.00 C 9826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.80 Conformation dependent library (CDL) restraints added in 2.8 seconds 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3556 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 8 sheets defined 62.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 4.167A pdb=" N LEU A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.571A pdb=" N ILE A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 4.003A pdb=" N LEU A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.180A pdb=" N GLU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 126 removed outlier: 5.298A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 162 through 191 removed outlier: 3.633A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 228 removed outlier: 4.364A pdb=" N PHE A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 283 through 316 Processing helix chain 'A' and resid 324 through 352 removed outlier: 4.128A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 361 through 369 removed outlier: 4.121A pdb=" N LEU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 389 Processing helix chain 'A' and resid 397 through 429 removed outlier: 3.661A pdb=" N SER A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 459 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 507 through 527 removed outlier: 3.730A pdb=" N ARG A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 removed outlier: 4.163A pdb=" N ASP A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 562 Processing helix chain 'A' and resid 569 through 575 removed outlier: 3.531A pdb=" N ARG A 572 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 575 " --> pdb=" O ARG A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 617 removed outlier: 3.664A pdb=" N THR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 593 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 647 removed outlier: 4.155A pdb=" N GLU A 635 " --> pdb=" O ASN A 631 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 678 removed outlier: 3.884A pdb=" N LYS A 677 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 678 " --> pdb=" O ASN A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 702 Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.845A pdb=" N ASN A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 723 No H-bonds generated for 'chain 'A' and resid 720 through 723' Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 832 through 846 removed outlier: 3.832A pdb=" N LEU A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'A' and resid 914 through 917 No H-bonds generated for 'chain 'A' and resid 914 through 917' Processing helix chain 'A' and resid 980 through 982 No H-bonds generated for 'chain 'A' and resid 980 through 982' Processing helix chain 'A' and resid 1011 through 1020 Processing helix chain 'B' and resid 8 through 28 removed outlier: 4.167A pdb=" N LEU B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.571A pdb=" N ILE B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 removed outlier: 4.003A pdb=" N LEU B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) Proline residue: B 82 - end of helix removed outlier: 4.180A pdb=" N GLU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 126 removed outlier: 5.298A pdb=" N ALA B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 162 through 191 removed outlier: 3.634A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 228 removed outlier: 4.364A pdb=" N PHE B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 253 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 277 No H-bonds generated for 'chain 'B' and resid 274 through 277' Processing helix chain 'B' and resid 283 through 316 Processing helix chain 'B' and resid 324 through 352 removed outlier: 4.128A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 361 through 369 removed outlier: 4.122A pdb=" N LEU B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 389 Processing helix chain 'B' and resid 397 through 429 removed outlier: 3.661A pdb=" N SER B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN B 423 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 459 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 507 through 527 removed outlier: 3.730A pdb=" N ARG B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 548 removed outlier: 4.163A pdb=" N ASP B 548 " --> pdb=" O ASP B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 569 through 575 removed outlier: 3.531A pdb=" N ARG B 572 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 575 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 617 removed outlier: 3.664A pdb=" N THR B 588 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 593 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 647 removed outlier: 4.155A pdb=" N GLU B 635 " --> pdb=" O ASN B 631 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 678 removed outlier: 3.884A pdb=" N LYS B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 678 " --> pdb=" O ASN B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 702 Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.845A pdb=" N ASN B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 723 No H-bonds generated for 'chain 'B' and resid 720 through 723' Processing helix chain 'B' and resid 731 through 734 No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 832 through 846 removed outlier: 3.832A pdb=" N LEU B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 864 Processing helix chain 'B' and resid 914 through 917 No H-bonds generated for 'chain 'B' and resid 914 through 917' Processing helix chain 'B' and resid 980 through 982 No H-bonds generated for 'chain 'B' and resid 980 through 982' Processing helix chain 'B' and resid 1011 through 1020 Processing sheet with id= A, first strand: chain 'A' and resid 740 through 742 removed outlier: 3.620A pdb=" N ILE A 763 " --> pdb=" O HIS A 811 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE A 813 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL A 761 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE A 815 " --> pdb=" O TRP A 759 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TRP A 759 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 766 through 769 Processing sheet with id= C, first strand: chain 'A' and resid 868 through 872 Processing sheet with id= D, first strand: chain 'A' and resid 906 through 908 Processing sheet with id= E, first strand: chain 'B' and resid 740 through 742 removed outlier: 3.620A pdb=" N ILE B 763 " --> pdb=" O HIS B 811 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE B 813 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL B 761 " --> pdb=" O PHE B 813 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE B 815 " --> pdb=" O TRP B 759 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TRP B 759 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 766 through 769 Processing sheet with id= G, first strand: chain 'B' and resid 868 through 872 Processing sheet with id= H, first strand: chain 'B' and resid 906 through 908 852 hydrogen bonds defined for protein. 2406 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: 4.80 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2398 1.30 - 1.43: 3942 1.43 - 1.56: 8960 1.56 - 1.69: 4 1.69 - 1.82: 124 Bond restraints: 15428 Sorted by residual: bond pdb=" C ASP A 731 " pdb=" O ASP A 731 " ideal model delta sigma weight residual 1.241 1.173 0.068 9.80e-03 1.04e+04 4.85e+01 bond pdb=" C ASP B 731 " pdb=" O ASP B 731 " ideal model delta sigma weight residual 1.241 1.173 0.068 9.80e-03 1.04e+04 4.81e+01 bond pdb=" C ASN B 418 " pdb=" O ASN B 418 " ideal model delta sigma weight residual 1.236 1.179 0.058 1.15e-02 7.56e+03 2.54e+01 bond pdb=" C ASN A 418 " pdb=" O ASN A 418 " ideal model delta sigma weight residual 1.236 1.179 0.058 1.15e-02 7.56e+03 2.52e+01 bond pdb=" C LEU A 119 " pdb=" O LEU A 119 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.26e+01 ... (remaining 15423 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.66: 483 106.66 - 113.48: 8448 113.48 - 120.31: 6019 120.31 - 127.14: 5790 127.14 - 133.97: 162 Bond angle restraints: 20902 Sorted by residual: angle pdb=" N GLN A 575 " pdb=" CA GLN A 575 " pdb=" C GLN A 575 " ideal model delta sigma weight residual 111.36 101.41 9.95 1.09e+00 8.42e-01 8.33e+01 angle pdb=" N GLN B 575 " pdb=" CA GLN B 575 " pdb=" C GLN B 575 " ideal model delta sigma weight residual 111.36 101.45 9.91 1.09e+00 8.42e-01 8.27e+01 angle pdb=" N GLU B 831 " pdb=" CA GLU B 831 " pdb=" C GLU B 831 " ideal model delta sigma weight residual 113.12 103.58 9.54 1.25e+00 6.40e-01 5.83e+01 angle pdb=" N GLU A 831 " pdb=" CA GLU A 831 " pdb=" C GLU A 831 " ideal model delta sigma weight residual 113.12 103.58 9.54 1.25e+00 6.40e-01 5.83e+01 angle pdb=" CA LEU B 733 " pdb=" C LEU B 733 " pdb=" O LEU B 733 " ideal model delta sigma weight residual 120.82 113.48 7.34 1.05e+00 9.07e-01 4.89e+01 ... (remaining 20897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 8594 25.33 - 50.67: 534 50.67 - 76.00: 54 76.00 - 101.34: 12 101.34 - 126.67: 2 Dihedral angle restraints: 9196 sinusoidal: 3680 harmonic: 5516 Sorted by residual: dihedral pdb=" C GLN B 676 " pdb=" N GLN B 676 " pdb=" CA GLN B 676 " pdb=" CB GLN B 676 " ideal model delta harmonic sigma weight residual -122.60 -111.81 -10.79 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" C GLN A 676 " pdb=" N GLN A 676 " pdb=" CA GLN A 676 " pdb=" CB GLN A 676 " ideal model delta harmonic sigma weight residual -122.60 -111.83 -10.77 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C37 46E A1201 " pdb=" C38 46E A1201 " pdb=" C39 46E A1201 " pdb=" C3A 46E A1201 " ideal model delta sinusoidal sigma weight residual 178.43 -54.90 -126.67 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 9193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2099 0.075 - 0.149: 237 0.149 - 0.224: 81 0.224 - 0.299: 29 0.299 - 0.374: 6 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA ILE A 815 " pdb=" N ILE A 815 " pdb=" C ILE A 815 " pdb=" CB ILE A 815 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA ILE B 815 " pdb=" N ILE B 815 " pdb=" C ILE B 815 " pdb=" CB ILE B 815 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ILE B 805 " pdb=" N ILE B 805 " pdb=" C ILE B 805 " pdb=" CB ILE B 805 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 2449 not shown) Planarity restraints: 2594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 894 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C LYS B 894 " -0.076 2.00e-02 2.50e+03 pdb=" O LYS B 894 " 0.029 2.00e-02 2.50e+03 pdb=" N THR B 895 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 894 " 0.021 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C LYS A 894 " -0.076 2.00e-02 2.50e+03 pdb=" O LYS A 894 " 0.029 2.00e-02 2.50e+03 pdb=" N THR A 895 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 733 " 0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU A 733 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU A 733 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU A 734 " 0.026 2.00e-02 2.50e+03 ... (remaining 2591 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1782 2.75 - 3.28: 15158 3.28 - 3.82: 23977 3.82 - 4.36: 29488 4.36 - 4.90: 51729 Nonbonded interactions: 122134 Sorted by model distance: nonbonded pdb=" O LYS B 699 " pdb=" OD1 ASN B 703 " model vdw 2.207 3.040 nonbonded pdb=" O LYS A 699 " pdb=" OD1 ASN A 703 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP A 696 " pdb=" OG1 THR B 480 " model vdw 2.244 2.440 nonbonded pdb=" O SER A 282 " pdb=" OG SER A 282 " model vdw 2.260 2.440 nonbonded pdb=" O SER B 282 " pdb=" OG SER B 282 " model vdw 2.260 2.440 ... (remaining 122129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 1.230 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: 4.390 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 43.140 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.007 0.071 15428 Z= 0.435 Angle : 1.110 10.951 20902 Z= 0.813 Chirality : 0.063 0.374 2452 Planarity : 0.006 0.049 2594 Dihedral : 15.580 126.673 5640 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.53 % Allowed : 14.15 % Favored : 84.31 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 1896 helix: -0.59 (0.14), residues: 1220 sheet: 0.54 (0.48), residues: 92 loop : -2.35 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 759 HIS 0.017 0.001 HIS A 319 PHE 0.029 0.002 PHE A 814 TYR 0.009 0.001 TYR A 800 ARG 0.005 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 292 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 311 average time/residue: 0.2847 time to fit residues: 127.1900 Evaluate side-chains 213 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 201 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 761 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 57 optimal weight: 0.0770 chunk 90 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 394 HIS A 418 ASN A 870 ASN B 298 ASN B 394 HIS B 673 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15428 Z= 0.193 Angle : 0.549 7.525 20902 Z= 0.284 Chirality : 0.038 0.132 2452 Planarity : 0.004 0.040 2594 Dihedral : 8.739 126.555 2158 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.49 % Allowed : 17.03 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 1896 helix: 0.80 (0.15), residues: 1244 sheet: 1.04 (0.53), residues: 82 loop : -1.76 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 985 HIS 0.005 0.001 HIS A 606 PHE 0.010 0.001 PHE B 616 TYR 0.015 0.001 TYR A 586 ARG 0.007 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 232 time to evaluate : 1.774 Fit side-chains REVERT: A 323 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.5988 (m-70) REVERT: B 323 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.5975 (m-70) outliers start: 57 outliers final: 24 residues processed: 260 average time/residue: 0.2757 time to fit residues: 106.8970 Evaluate side-chains 231 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 0.0670 chunk 143 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 897 ASN B 338 GLN B 897 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15428 Z= 0.275 Angle : 0.543 6.569 20902 Z= 0.283 Chirality : 0.040 0.218 2452 Planarity : 0.004 0.036 2594 Dihedral : 8.251 107.919 2140 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.80 % Allowed : 17.40 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1896 helix: 1.44 (0.15), residues: 1240 sheet: 1.34 (0.57), residues: 72 loop : -1.36 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 985 HIS 0.006 0.001 HIS B 95 PHE 0.025 0.001 PHE B 195 TYR 0.011 0.001 TYR B 187 ARG 0.005 0.000 ARG B 866 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 199 time to evaluate : 1.689 Fit side-chains revert: symmetry clash REVERT: A 323 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6182 (m-70) REVERT: B 323 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6191 (m-70) outliers start: 62 outliers final: 41 residues processed: 235 average time/residue: 0.2473 time to fit residues: 87.8630 Evaluate side-chains 231 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 930 CYS Chi-restraints excluded: chain B residue 1019 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 96 GLN A 338 GLN B 70 ASN B 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15428 Z= 0.218 Angle : 0.511 7.690 20902 Z= 0.265 Chirality : 0.038 0.160 2452 Planarity : 0.004 0.037 2594 Dihedral : 7.801 87.785 2140 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.82 % Allowed : 19.42 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1896 helix: 1.84 (0.15), residues: 1232 sheet: 1.37 (0.58), residues: 72 loop : -1.28 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 985 HIS 0.005 0.001 HIS A 319 PHE 0.009 0.001 PHE A 117 TYR 0.010 0.001 TYR A 570 ARG 0.004 0.000 ARG B 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 1.797 Fit side-chains REVERT: A 323 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.6001 (m-70) REVERT: B 323 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.5964 (m-70) outliers start: 46 outliers final: 36 residues processed: 230 average time/residue: 0.2543 time to fit residues: 89.4128 Evaluate side-chains 224 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 930 CYS Chi-restraints excluded: chain B residue 1019 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.0020 chunk 104 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15428 Z= 0.169 Angle : 0.496 7.882 20902 Z= 0.255 Chirality : 0.038 0.161 2452 Planarity : 0.004 0.038 2594 Dihedral : 7.526 86.348 2140 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.76 % Allowed : 20.53 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1896 helix: 2.04 (0.15), residues: 1236 sheet: 1.41 (0.59), residues: 72 loop : -1.26 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 985 HIS 0.005 0.001 HIS B 319 PHE 0.016 0.001 PHE A 228 TYR 0.009 0.001 TYR B 570 ARG 0.004 0.000 ARG B 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 1.840 Fit side-chains revert: symmetry clash REVERT: A 323 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.5934 (m-70) REVERT: B 323 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.5915 (m-70) outliers start: 45 outliers final: 30 residues processed: 242 average time/residue: 0.2369 time to fit residues: 88.4326 Evaluate side-chains 224 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1019 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN A 674 ASN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 674 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15428 Z= 0.189 Angle : 0.511 11.094 20902 Z= 0.261 Chirality : 0.038 0.132 2452 Planarity : 0.004 0.040 2594 Dihedral : 7.421 85.217 2140 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.57 % Allowed : 21.51 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1896 helix: 2.16 (0.16), residues: 1218 sheet: 1.50 (0.60), residues: 72 loop : -1.26 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 985 HIS 0.005 0.001 HIS A 606 PHE 0.026 0.001 PHE A 195 TYR 0.010 0.001 TYR B 245 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 2.018 Fit side-chains revert: symmetry clash REVERT: A 323 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.6219 (m-70) REVERT: B 323 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6188 (m-70) REVERT: B 898 GLN cc_start: 0.6889 (mp10) cc_final: 0.6676 (pm20) outliers start: 42 outliers final: 34 residues processed: 225 average time/residue: 0.2501 time to fit residues: 85.6262 Evaluate side-chains 232 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1019 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15428 Z= 0.147 Angle : 0.491 8.419 20902 Z= 0.250 Chirality : 0.037 0.121 2452 Planarity : 0.004 0.041 2594 Dihedral : 7.221 87.304 2140 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.84 % Allowed : 22.12 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.20), residues: 1896 helix: 2.29 (0.15), residues: 1210 sheet: 1.60 (0.60), residues: 72 loop : -1.26 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 985 HIS 0.004 0.001 HIS A 606 PHE 0.013 0.001 PHE A 228 TYR 0.009 0.001 TYR B 245 ARG 0.004 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 1.816 Fit side-chains revert: symmetry clash REVERT: A 323 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.6220 (m-70) REVERT: B 323 HIS cc_start: 0.6672 (OUTLIER) cc_final: 0.6181 (m-70) outliers start: 30 outliers final: 21 residues processed: 229 average time/residue: 0.2468 time to fit residues: 85.3998 Evaluate side-chains 226 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 947 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.5980 chunk 109 optimal weight: 0.0470 chunk 55 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15428 Z= 0.263 Angle : 0.542 8.414 20902 Z= 0.278 Chirality : 0.039 0.185 2452 Planarity : 0.004 0.049 2594 Dihedral : 7.404 86.946 2140 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.90 % Allowed : 22.24 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1896 helix: 2.27 (0.15), residues: 1210 sheet: 1.56 (0.59), residues: 72 loop : -1.13 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 985 HIS 0.008 0.001 HIS A 288 PHE 0.014 0.001 PHE B 117 TYR 0.012 0.001 TYR A 245 ARG 0.012 0.000 ARG B 866 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 323 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6378 (m-70) REVERT: B 323 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6385 (m-70) outliers start: 31 outliers final: 28 residues processed: 206 average time/residue: 0.2661 time to fit residues: 82.4015 Evaluate side-chains 213 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1019 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.0010 chunk 170 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 154 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15428 Z= 0.169 Angle : 0.510 11.696 20902 Z= 0.259 Chirality : 0.037 0.179 2452 Planarity : 0.004 0.040 2594 Dihedral : 7.250 88.055 2140 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.84 % Allowed : 22.24 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.20), residues: 1896 helix: 2.40 (0.15), residues: 1206 sheet: 1.61 (0.60), residues: 72 loop : -1.17 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 985 HIS 0.006 0.001 HIS B 288 PHE 0.012 0.001 PHE A 228 TYR 0.010 0.001 TYR A 245 ARG 0.008 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.783 Fit side-chains revert: symmetry clash REVERT: A 323 HIS cc_start: 0.6833 (OUTLIER) cc_final: 0.6355 (m-70) REVERT: B 104 MET cc_start: 0.7917 (tpp) cc_final: 0.7564 (mpp) REVERT: B 323 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.6377 (m-70) outliers start: 30 outliers final: 23 residues processed: 217 average time/residue: 0.2663 time to fit residues: 86.9183 Evaluate side-chains 217 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1019 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 160 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN B 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15428 Z= 0.281 Angle : 0.562 11.297 20902 Z= 0.285 Chirality : 0.040 0.212 2452 Planarity : 0.004 0.038 2594 Dihedral : 7.234 88.762 2140 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.84 % Allowed : 22.24 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.20), residues: 1896 helix: 2.35 (0.15), residues: 1210 sheet: 1.53 (0.60), residues: 72 loop : -1.10 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 985 HIS 0.007 0.001 HIS B 288 PHE 0.014 0.001 PHE B 117 TYR 0.011 0.001 TYR B 245 ARG 0.006 0.000 ARG B 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.967 Fit side-chains REVERT: A 323 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6447 (m-70) REVERT: A 686 MET cc_start: 0.7090 (tpp) cc_final: 0.6771 (tpt) REVERT: B 104 MET cc_start: 0.7966 (tpp) cc_final: 0.7595 (mpp) REVERT: B 323 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6484 (m-70) outliers start: 30 outliers final: 27 residues processed: 191 average time/residue: 0.2659 time to fit residues: 77.1383 Evaluate side-chains 197 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 1019 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.072182 restraints weight = 30730.251| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.44 r_work: 0.2730 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15428 Z= 0.192 Angle : 0.526 10.131 20902 Z= 0.268 Chirality : 0.038 0.190 2452 Planarity : 0.004 0.041 2594 Dihedral : 6.994 89.618 2140 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.72 % Allowed : 22.67 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 1896 helix: 2.44 (0.15), residues: 1206 sheet: 1.54 (0.59), residues: 72 loop : -1.08 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 985 HIS 0.006 0.001 HIS A 288 PHE 0.013 0.001 PHE A 228 TYR 0.010 0.001 TYR B 245 ARG 0.008 0.000 ARG B 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3113.61 seconds wall clock time: 56 minutes 53.76 seconds (3413.76 seconds total)