Starting phenix.real_space_refine on Thu Mar 14 22:19:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/03_2024/8k3p_36855_updated.pdb" } resolution = 3.64 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= -0.000 sd= 0.023 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 57 5.16 5 C 6464 2.51 5 N 1605 2.21 5 O 1778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 412": "OE1" <-> "OE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 610": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1066": "OD1" <-> "OD2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 610": "OD1" <-> "OD2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 717": "OD1" <-> "OD2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 862": "OE1" <-> "OE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1066": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9906 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 4856 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 18, 'TRANS': 641} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 532 Unresolved non-hydrogen angles: 656 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 299 Chain: "B" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 4884 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 18, 'TRANS': 641} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 502 Unresolved non-hydrogen angles: 616 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 10, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 279 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'POV': 1, 'VDG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'POV': 1, 'VDG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.58, per 1000 atoms: 0.56 Number of scatterers: 9906 At special positions: 0 Unit cell: (79.5, 134.62, 104.94, 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 57 16.00 P 2 15.00 O 1778 8.00 N 1605 7.00 C 6464 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: 4.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 8 sheets defined 58.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 411 through 414 No H-bonds generated for 'chain 'A' and resid 411 through 414' Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 436 through 439 No H-bonds generated for 'chain 'A' and resid 436 through 439' Processing helix chain 'A' and resid 459 through 478 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 507 through 516 removed outlier: 4.306A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 611 through 620 removed outlier: 3.871A pdb=" N PHE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG A 620 " --> pdb=" O TRP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 645 through 658 Processing helix chain 'A' and resid 661 through 668 removed outlier: 3.636A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 686 No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 707 through 715 removed outlier: 6.301A pdb=" N TYR A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 750 through 780 removed outlier: 4.473A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG A 777 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP A 779 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 806 Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 831 through 855 Processing helix chain 'A' and resid 863 through 894 Processing helix chain 'A' and resid 909 through 932 Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 942 through 954 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 956 through 962 Processing helix chain 'A' and resid 1028 through 1059 removed outlier: 3.604A pdb=" N VAL A1043 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1074 Processing helix chain 'A' and resid 1092 through 1128 removed outlier: 3.573A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 411 through 414 No H-bonds generated for 'chain 'B' and resid 411 through 414' Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 436 through 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 459 through 478 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 507 through 516 removed outlier: 4.307A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 585 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 620 removed outlier: 3.871A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 620 " --> pdb=" O TRP B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 643 removed outlier: 5.901A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 658 Processing helix chain 'B' and resid 661 through 668 removed outlier: 3.636A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 686 No H-bonds generated for 'chain 'B' and resid 683 through 686' Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 707 through 715 removed outlier: 6.301A pdb=" N TYR B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 714 " --> pdb=" O SER B 710 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 725 Processing helix chain 'B' and resid 750 through 780 removed outlier: 4.473A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR B 776 " --> pdb=" O PHE B 772 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG B 777 " --> pdb=" O CYS B 773 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL B 778 " --> pdb=" O HIS B 774 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP B 779 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER B 780 " --> pdb=" O TYR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 806 Processing helix chain 'B' and resid 808 through 827 Processing helix chain 'B' and resid 831 through 855 Processing helix chain 'B' and resid 863 through 894 Processing helix chain 'B' and resid 909 through 932 Processing helix chain 'B' and resid 937 through 939 No H-bonds generated for 'chain 'B' and resid 937 through 939' Processing helix chain 'B' and resid 942 through 954 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 956 through 962 Processing helix chain 'B' and resid 1028 through 1059 removed outlier: 3.605A pdb=" N VAL B1043 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1074 Processing helix chain 'B' and resid 1092 through 1128 removed outlier: 3.572A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 386 through 390 removed outlier: 4.454A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 607 removed outlier: 5.893A pdb=" N GLU A 630 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR A 744 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG A 632 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.908A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 624 through 628 removed outlier: 7.244A pdb=" N ILE A 733 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA A 627 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS A 735 " --> pdb=" O ALA A 627 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 386 through 390 removed outlier: 4.397A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 605 through 607 removed outlier: 6.675A pdb=" N GLU B 630 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR B 744 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 632 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.908A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 624 through 629 removed outlier: 7.244A pdb=" N ILE B 733 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA B 627 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS B 735 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY B 629 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS B 737 " --> pdb=" O GLY B 629 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 568 hydrogen bonds defined for protein. 1674 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: 3.23 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1518 1.28 - 1.41: 2742 1.41 - 1.54: 5779 1.54 - 1.68: 11 1.68 - 1.81: 84 Bond restraints: 10134 Sorted by residual: bond pdb=" C19 VDG B1302 " pdb=" C20 VDG B1302 " ideal model delta sigma weight residual 1.346 1.593 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C19 VDG A1302 " pdb=" C20 VDG A1302 " ideal model delta sigma weight residual 1.346 1.593 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C19 VDG A1302 " pdb=" O01 VDG A1302 " ideal model delta sigma weight residual 1.518 1.273 0.245 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C19 VDG B1302 " pdb=" O01 VDG B1302 " ideal model delta sigma weight residual 1.518 1.273 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C26 VDG A1302 " pdb=" N16 VDG A1302 " ideal model delta sigma weight residual 1.502 1.316 0.186 2.00e-02 2.50e+03 8.68e+01 ... (remaining 10129 not shown) Histogram of bond angle deviations from ideal: 94.74 - 102.64: 35 102.64 - 110.55: 2852 110.55 - 118.45: 5216 118.45 - 126.36: 5602 126.36 - 134.26: 125 Bond angle restraints: 13830 Sorted by residual: angle pdb=" CA GLY A 636 " pdb=" C GLY A 636 " pdb=" O GLY A 636 " ideal model delta sigma weight residual 122.57 118.23 4.34 9.20e-01 1.18e+00 2.23e+01 angle pdb=" C LEU B 635 " pdb=" CA LEU B 635 " pdb=" CB LEU B 635 " ideal model delta sigma weight residual 116.54 111.53 5.01 1.15e+00 7.56e-01 1.90e+01 angle pdb=" CA ILE A 391 " pdb=" C ILE A 391 " pdb=" O ILE A 391 " ideal model delta sigma weight residual 121.97 118.21 3.76 9.80e-01 1.04e+00 1.47e+01 angle pdb=" CA ILE B 391 " pdb=" C ILE B 391 " pdb=" O ILE B 391 " ideal model delta sigma weight residual 121.97 118.22 3.75 9.80e-01 1.04e+00 1.47e+01 angle pdb=" N PRO B 425 " pdb=" CA PRO B 425 " pdb=" C PRO B 425 " ideal model delta sigma weight residual 112.47 119.79 -7.32 2.06e+00 2.36e-01 1.26e+01 ... (remaining 13825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.48: 5729 33.48 - 66.97: 118 66.97 - 100.45: 11 100.45 - 133.94: 2 133.94 - 167.42: 2 Dihedral angle restraints: 5862 sinusoidal: 1966 harmonic: 3896 Sorted by residual: dihedral pdb=" C27 POV A1301 " pdb=" C28 POV A1301 " pdb=" C29 POV A1301 " pdb="C210 POV A1301 " ideal model delta sinusoidal sigma weight residual 127.48 -65.10 -167.42 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C27 POV B1301 " pdb=" C28 POV B1301 " pdb=" C29 POV B1301 " pdb="C210 POV B1301 " ideal model delta sinusoidal sigma weight residual 127.48 -65.12 -167.40 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C29 POV B1301 " pdb="C210 POV B1301 " pdb="C211 POV B1301 " pdb="C212 POV B1301 " ideal model delta sinusoidal sigma weight residual 112.25 -121.65 -126.10 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 5859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 937 0.041 - 0.081: 369 0.081 - 0.122: 196 0.122 - 0.162: 94 0.162 - 0.203: 40 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CA LEU B 734 " pdb=" N LEU B 734 " pdb=" C LEU B 734 " pdb=" CB LEU B 734 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU A 734 " pdb=" N LEU A 734 " pdb=" C LEU A 734 " pdb=" CB LEU A 734 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE B 946 " pdb=" N ILE B 946 " pdb=" C ILE B 946 " pdb=" CB ILE B 946 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 1633 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 424 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C GLU B 424 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU B 424 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO B 425 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 424 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C GLU A 424 " 0.054 2.00e-02 2.50e+03 pdb=" O GLU A 424 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 425 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1301 " -0.020 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C29 POV B1301 " 0.020 2.00e-02 2.50e+03 pdb="C210 POV B1301 " 0.020 2.00e-02 2.50e+03 pdb="C211 POV B1301 " -0.020 2.00e-02 2.50e+03 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2901 2.81 - 3.34: 10433 3.34 - 3.86: 16399 3.86 - 4.38: 17735 4.38 - 4.90: 29885 Nonbonded interactions: 77353 Sorted by model distance: nonbonded pdb=" O ALA B1069 " pdb=" OG SER B1072 " model vdw 2.293 2.440 nonbonded pdb=" O ALA A1069 " pdb=" OG SER A1072 " model vdw 2.293 2.440 nonbonded pdb=" O SER A1072 " pdb=" OG1 THR A1075 " model vdw 2.302 2.440 nonbonded pdb=" O SER B1072 " pdb=" OG1 THR B1075 " model vdw 2.302 2.440 nonbonded pdb=" O VAL A 421 " pdb=" N ALA A 534 " model vdw 2.371 2.520 ... (remaining 77348 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' and (resid 382 through 577 or (resid 578 and (name N or name CA or na \ me C or name O or name CB )) or resid 579 through 1129 or resid 1301 through 130 \ 2)) selection = (chain 'B' and (resid 382 through 489 or (resid 490 through 492 and (name N or n \ ame CA or name C or name O or name CB )) or resid 493 through 575 or (resid 576 \ through 578 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 9 or (resid 580 and (name N or name CA or name C or name O or name CB )) or resi \ d 581 through 605 or (resid 606 and (name N or name CA or name C or name O or na \ me CB )) or resid 607 through 634 or (resid 635 and (name N or name CA or name C \ or name O or name CB )) or (resid 636 through 641 and (name N or name CA or nam \ e C or name O or name CB )) or resid 642 through 652 or (resid 653 and (name N o \ r name CA or name C or name O or name CB )) or resid 654 through 1129 or resid 1 \ 301 through 1302)) } 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: 0.490 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: 2.790 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.980 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.010 0.247 10134 Z= 0.654 Angle : 0.925 8.459 13830 Z= 0.662 Chirality : 0.065 0.203 1636 Planarity : 0.004 0.032 1708 Dihedral : 15.193 167.421 3342 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.22 % Allowed : 2.68 % Favored : 94.11 % 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: 0.23 (0.23), residues: 1300 helix: 0.98 (0.19), residues: 754 sheet: -0.74 (0.39), residues: 168 loop : -0.93 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1103 HIS 0.002 0.001 HIS B 582 PHE 0.011 0.001 PHE A 885 TYR 0.033 0.002 TYR B1097 ARG 0.006 0.001 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 1.168 Fit side-chains REVERT: A 535 MET cc_start: 0.7965 (ttp) cc_final: 0.7664 (ttp) REVERT: A 583 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8246 (ttm-80) REVERT: B 606 MET cc_start: 0.8388 (mmt) cc_final: 0.8082 (mmp) outliers start: 30 outliers final: 4 residues processed: 210 average time/residue: 0.1702 time to fit residues: 53.6806 Evaluate side-chains 140 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 942 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS A 472 ASN A 582 HIS A 650 GLN A 658 ASN B 459 HIS B 472 ASN B 658 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10134 Z= 0.193 Angle : 0.530 6.793 13830 Z= 0.281 Chirality : 0.041 0.144 1636 Planarity : 0.003 0.030 1708 Dihedral : 11.944 146.643 1525 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.79 % Allowed : 9.86 % Favored : 87.35 % 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: 1.37 (0.24), residues: 1300 helix: 2.07 (0.19), residues: 756 sheet: -0.41 (0.39), residues: 160 loop : -0.87 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1103 HIS 0.003 0.001 HIS A 582 PHE 0.020 0.002 PHE B1124 TYR 0.014 0.001 TYR B1097 ARG 0.003 0.000 ARG B1112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 814 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8030 (tp) REVERT: A 1070 MET cc_start: 0.8131 (tmm) cc_final: 0.7823 (tmm) REVERT: A 1112 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7554 (mtm110) REVERT: B 1112 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7455 (mtm180) outliers start: 26 outliers final: 18 residues processed: 183 average time/residue: 0.1610 time to fit residues: 44.8590 Evaluate side-chains 159 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 119 optimal weight: 0.0370 chunk 40 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10134 Z= 0.140 Angle : 0.474 6.333 13830 Z= 0.250 Chirality : 0.040 0.141 1636 Planarity : 0.003 0.031 1708 Dihedral : 11.722 166.777 1525 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.11 % Allowed : 12.22 % Favored : 84.67 % 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: 1.82 (0.24), residues: 1300 helix: 2.40 (0.19), residues: 756 sheet: -0.10 (0.39), residues: 160 loop : -0.64 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 PHE 0.025 0.001 PHE B 569 TYR 0.011 0.001 TYR B1067 ARG 0.002 0.000 ARG B1112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 510 LEU cc_start: 0.9134 (mt) cc_final: 0.8925 (mt) REVERT: A 535 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7257 (ttp) REVERT: A 571 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 692 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8402 (tp40) REVERT: A 814 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 832 ASN cc_start: 0.6647 (OUTLIER) cc_final: 0.6408 (m-40) REVERT: A 850 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.7894 (t80) REVERT: A 1112 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7569 (mtm110) REVERT: B 653 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8331 (tp30) REVERT: B 814 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8211 (tp) REVERT: B 832 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6496 (m-40) REVERT: B 1112 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7677 (mtm110) outliers start: 29 outliers final: 14 residues processed: 168 average time/residue: 0.1654 time to fit residues: 42.5015 Evaluate side-chains 159 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10134 Z= 0.324 Angle : 0.562 7.316 13830 Z= 0.301 Chirality : 0.042 0.148 1636 Planarity : 0.003 0.029 1708 Dihedral : 11.850 177.146 1523 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.29 % Allowed : 14.36 % Favored : 81.35 % 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: 1.70 (0.23), residues: 1300 helix: 2.30 (0.19), residues: 746 sheet: -0.26 (0.38), residues: 160 loop : -0.55 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 490 HIS 0.006 0.001 HIS A 459 PHE 0.021 0.002 PHE B 813 TYR 0.021 0.002 TYR B 878 ARG 0.003 0.001 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 535 MET cc_start: 0.7870 (ttp) cc_final: 0.7471 (ttp) REVERT: A 692 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8542 (tp40) REVERT: A 792 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 832 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6466 (m-40) REVERT: A 867 LEU cc_start: 0.9012 (tp) cc_final: 0.8793 (tp) REVERT: A 1070 MET cc_start: 0.8142 (tmm) cc_final: 0.7563 (tmm) REVERT: A 1112 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7732 (mtm110) REVERT: B 526 ASP cc_start: 0.8113 (p0) cc_final: 0.7640 (p0) REVERT: B 653 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8503 (tp30) REVERT: B 832 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6599 (m-40) outliers start: 40 outliers final: 29 residues processed: 162 average time/residue: 0.1524 time to fit residues: 38.6557 Evaluate side-chains 164 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 853 SER Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 42 optimal weight: 0.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10134 Z= 0.172 Angle : 0.464 6.690 13830 Z= 0.245 Chirality : 0.039 0.140 1636 Planarity : 0.003 0.030 1708 Dihedral : 10.261 134.276 1522 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.18 % Allowed : 16.29 % Favored : 79.53 % 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: 1.92 (0.23), residues: 1300 helix: 2.50 (0.19), residues: 744 sheet: -0.13 (0.40), residues: 156 loop : -0.51 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 490 HIS 0.004 0.001 HIS B 459 PHE 0.017 0.001 PHE B 569 TYR 0.019 0.001 TYR B1097 ARG 0.004 0.000 ARG B1112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 535 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7698 (ttp) REVERT: A 571 LEU cc_start: 0.9003 (tt) cc_final: 0.8767 (tt) REVERT: A 692 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8519 (tp40) REVERT: A 832 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6457 (m-40) REVERT: A 850 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8062 (t80) REVERT: A 1070 MET cc_start: 0.8227 (tmm) cc_final: 0.7764 (tmm) REVERT: A 1112 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7726 (mtm110) REVERT: B 653 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8526 (tp30) REVERT: B 832 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.6531 (m-40) REVERT: B 1070 MET cc_start: 0.8337 (tmm) cc_final: 0.7849 (tmm) outliers start: 39 outliers final: 27 residues processed: 166 average time/residue: 0.1512 time to fit residues: 39.7056 Evaluate side-chains 161 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 853 SER Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 127 optimal weight: 0.0070 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10134 Z= 0.126 Angle : 0.441 6.658 13830 Z= 0.231 Chirality : 0.038 0.140 1636 Planarity : 0.003 0.029 1708 Dihedral : 9.374 81.031 1522 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.89 % Allowed : 17.58 % Favored : 79.53 % 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: 2.07 (0.24), residues: 1300 helix: 2.60 (0.19), residues: 742 sheet: -0.25 (0.39), residues: 162 loop : -0.29 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 PHE 0.015 0.001 PHE B 569 TYR 0.011 0.001 TYR A 827 ARG 0.003 0.000 ARG B1112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 535 MET cc_start: 0.8069 (ttp) cc_final: 0.7739 (ttp) REVERT: A 571 LEU cc_start: 0.9023 (tt) cc_final: 0.8764 (tt) REVERT: A 692 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8481 (tp40) REVERT: A 832 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.6495 (m-40) REVERT: A 850 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8095 (t80) REVERT: A 1070 MET cc_start: 0.8221 (tmm) cc_final: 0.7818 (tmm) REVERT: A 1112 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7689 (mtm110) REVERT: B 606 MET cc_start: 0.7976 (mmp) cc_final: 0.7734 (mmp) REVERT: B 653 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8504 (tp30) REVERT: B 832 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6568 (m-40) REVERT: B 1070 MET cc_start: 0.8308 (tmm) cc_final: 0.8025 (tmm) outliers start: 27 outliers final: 21 residues processed: 164 average time/residue: 0.1565 time to fit residues: 40.2485 Evaluate side-chains 160 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1073 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.0170 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 71 optimal weight: 0.0770 chunk 127 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10134 Z= 0.111 Angle : 0.430 6.109 13830 Z= 0.223 Chirality : 0.038 0.142 1636 Planarity : 0.003 0.029 1708 Dihedral : 9.087 79.130 1522 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.32 % Allowed : 18.33 % Favored : 78.35 % 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: 2.13 (0.24), residues: 1300 helix: 2.64 (0.19), residues: 742 sheet: -0.23 (0.39), residues: 162 loop : -0.24 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 490 HIS 0.005 0.001 HIS B 459 PHE 0.015 0.001 PHE B 885 TYR 0.011 0.001 TYR A 519 ARG 0.003 0.000 ARG B1112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 692 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8427 (tp40) REVERT: A 738 ARG cc_start: 0.8385 (ptm-80) cc_final: 0.7937 (ptm-80) REVERT: A 799 PHE cc_start: 0.8329 (t80) cc_final: 0.8004 (t80) REVERT: A 832 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6506 (m-40) REVERT: A 850 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8125 (t80) REVERT: A 1070 MET cc_start: 0.8244 (tmm) cc_final: 0.7929 (tmm) REVERT: B 653 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8490 (tp30) REVERT: B 799 PHE cc_start: 0.8352 (t80) cc_final: 0.7988 (t80) REVERT: B 832 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6516 (m-40) REVERT: B 1070 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: B 1112 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7601 (mtm180) outliers start: 31 outliers final: 20 residues processed: 178 average time/residue: 0.1561 time to fit residues: 43.2817 Evaluate side-chains 170 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 chunk 86 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10134 Z= 0.122 Angle : 0.432 5.951 13830 Z= 0.223 Chirality : 0.038 0.135 1636 Planarity : 0.003 0.030 1708 Dihedral : 8.936 75.584 1522 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.79 % Allowed : 18.44 % Favored : 78.78 % 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: 2.17 (0.24), residues: 1300 helix: 2.66 (0.19), residues: 742 sheet: -0.14 (0.40), residues: 162 loop : -0.21 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 490 HIS 0.004 0.001 HIS B 459 PHE 0.015 0.001 PHE B1124 TYR 0.016 0.001 TYR A 519 ARG 0.003 0.000 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.041 Fit side-chains REVERT: A 571 LEU cc_start: 0.8938 (tt) cc_final: 0.8671 (tt) REVERT: A 692 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8424 (tp40) REVERT: A 738 ARG cc_start: 0.8354 (ptm-80) cc_final: 0.7888 (ptm-80) REVERT: A 799 PHE cc_start: 0.8386 (t80) cc_final: 0.7996 (t80) REVERT: A 832 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6503 (m-40) REVERT: A 850 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8108 (t80) REVERT: A 1070 MET cc_start: 0.8240 (tmm) cc_final: 0.7981 (tmm) REVERT: B 653 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8476 (tp30) REVERT: B 738 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.7776 (ptm-80) REVERT: B 772 PHE cc_start: 0.8660 (t80) cc_final: 0.8151 (t80) REVERT: B 799 PHE cc_start: 0.8362 (t80) cc_final: 0.7824 (t80) REVERT: B 832 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6536 (m-40) REVERT: B 1070 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8089 (tmm) outliers start: 26 outliers final: 19 residues processed: 172 average time/residue: 0.1666 time to fit residues: 43.5109 Evaluate side-chains 170 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1073 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10134 Z= 0.261 Angle : 0.520 12.040 13830 Z= 0.266 Chirality : 0.040 0.174 1636 Planarity : 0.003 0.029 1708 Dihedral : 8.970 67.971 1522 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.32 % Allowed : 18.11 % Favored : 78.56 % 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: 2.05 (0.23), residues: 1300 helix: 2.58 (0.19), residues: 742 sheet: -0.32 (0.39), residues: 162 loop : -0.25 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.003 0.001 HIS A 774 PHE 0.016 0.001 PHE B 813 TYR 0.032 0.001 TYR A 519 ARG 0.006 0.000 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.054 Fit side-chains REVERT: A 535 MET cc_start: 0.7589 (ttp) cc_final: 0.7344 (ttp) REVERT: A 692 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8504 (tp40) REVERT: A 832 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6527 (m-40) REVERT: A 850 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8101 (t80) REVERT: A 1070 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7987 (tmm) REVERT: B 653 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8509 (tp30) REVERT: B 772 PHE cc_start: 0.8723 (t80) cc_final: 0.8471 (t80) REVERT: B 832 ASN cc_start: 0.7078 (OUTLIER) cc_final: 0.6707 (m-40) REVERT: B 1070 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7970 (tmm) outliers start: 31 outliers final: 24 residues processed: 166 average time/residue: 0.1488 time to fit residues: 38.8149 Evaluate side-chains 168 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10134 Z= 0.184 Angle : 0.485 11.242 13830 Z= 0.247 Chirality : 0.039 0.175 1636 Planarity : 0.003 0.029 1708 Dihedral : 8.800 67.078 1522 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.89 % Allowed : 18.54 % Favored : 78.56 % 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: 2.08 (0.24), residues: 1300 helix: 2.59 (0.19), residues: 742 sheet: -0.33 (0.39), residues: 162 loop : -0.21 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 490 HIS 0.004 0.001 HIS A 459 PHE 0.018 0.001 PHE B 569 TYR 0.031 0.001 TYR A 519 ARG 0.002 0.000 ARG A1112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.037 Fit side-chains REVERT: A 518 CYS cc_start: 0.8389 (m) cc_final: 0.8147 (t) REVERT: A 571 LEU cc_start: 0.8943 (tt) cc_final: 0.8690 (tt) REVERT: A 692 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8509 (tp40) REVERT: A 738 ARG cc_start: 0.8495 (ptm-80) cc_final: 0.8231 (ptm-80) REVERT: A 799 PHE cc_start: 0.8429 (t80) cc_final: 0.8022 (t80) REVERT: A 832 ASN cc_start: 0.6859 (OUTLIER) cc_final: 0.6546 (m-40) REVERT: A 1070 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7975 (tmm) REVERT: B 653 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8509 (tp30) REVERT: B 772 PHE cc_start: 0.8667 (t80) cc_final: 0.8137 (t80) REVERT: B 799 PHE cc_start: 0.8371 (t80) cc_final: 0.7780 (t80) REVERT: B 832 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6659 (m-40) REVERT: B 1070 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8079 (tmm) outliers start: 27 outliers final: 22 residues processed: 160 average time/residue: 0.1580 time to fit residues: 39.2275 Evaluate side-chains 166 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.0070 chunk 19 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 75 optimal weight: 0.0870 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096535 restraints weight = 19637.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099855 restraints weight = 9718.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102071 restraints weight = 6239.929| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10134 Z= 0.122 Angle : 0.452 7.083 13830 Z= 0.233 Chirality : 0.038 0.140 1636 Planarity : 0.003 0.032 1708 Dihedral : 8.546 67.399 1522 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.79 % Allowed : 18.86 % Favored : 78.35 % 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: 2.15 (0.24), residues: 1300 helix: 2.63 (0.19), residues: 746 sheet: -0.15 (0.40), residues: 162 loop : -0.26 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1103 HIS 0.005 0.001 HIS A 459 PHE 0.030 0.001 PHE B 569 TYR 0.026 0.001 TYR A 519 ARG 0.003 0.000 ARG B1112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.95 seconds wall clock time: 33 minutes 49.75 seconds (2029.75 seconds total)