Starting phenix.real_space_refine on Sat Dec 9 03:27:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/12_2023/8k3p_36855_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/12_2023/8k3p_36855.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/12_2023/8k3p_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_36855/12_2023/8k3p_36855_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/12_2023/8k3p_36855_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/12_2023/8k3p_36855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/12_2023/8k3p_36855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/12_2023/8k3p_36855_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3p_36855/12_2023/8k3p_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.64, per 1000 atoms: 0.57 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: 4.15 Conformation dependent library (CDL) restraints added in 1.8 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: 2.42 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: 3.08 Time building geometry restraints manager: 4.49 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: 1.040 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: 2.870 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.790 Find NCS groups from input model: 0.580 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- 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 : 1.220 Fit side-chains outliers start: 30 outliers final: 4 residues processed: 210 average time/residue: 0.1754 time to fit residues: 54.8831 Evaluate side-chains 139 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1018 time to fit residues: 2.3058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.0040 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: 5.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10134 Z= 0.174 Angle : 0.531 7.017 13830 Z= 0.280 Chirality : 0.041 0.142 1636 Planarity : 0.003 0.030 1708 Dihedral : 11.670 143.856 1518 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.47 % Allowed : 10.08 % Favored : 87.46 % 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: 1.50 (0.24), residues: 1300 helix: 2.20 (0.19), residues: 744 sheet: -0.41 (0.39), residues: 160 loop : -0.72 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1103 HIS 0.003 0.001 HIS B 459 PHE 0.020 0.002 PHE B1124 TYR 0.014 0.001 TYR B1097 ARG 0.004 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 191 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 182 average time/residue: 0.1936 time to fit residues: 54.1086 Evaluate side-chains 157 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0952 time to fit residues: 4.1385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 0.0020 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.5128 ------------------------------------------------------------------------------- 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: 0.7891 moved from start: 0.2070 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= 0.133 Angle : 0.468 5.995 13830 Z= 0.247 Chirality : 0.039 0.140 1636 Planarity : 0.003 0.027 1708 Dihedral : 11.470 157.430 1518 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.61 % Allowed : 12.54 % Favored : 85.85 % 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: 1.84 (0.24), residues: 1300 helix: 2.44 (0.19), residues: 756 sheet: -0.20 (0.39), residues: 160 loop : -0.64 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1103 HIS 0.005 0.001 HIS B 459 PHE 0.012 0.001 PHE A1052 TYR 0.015 0.001 TYR A1097 ARG 0.004 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 171 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.096 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 165 average time/residue: 0.1641 time to fit residues: 42.0856 Evaluate side-chains 145 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1067 time to fit residues: 2.7753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7948 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10134 Z= 0.184 Angle : 0.476 9.759 13830 Z= 0.251 Chirality : 0.039 0.143 1636 Planarity : 0.003 0.028 1708 Dihedral : 11.523 172.742 1518 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.14 % Allowed : 14.58 % Favored : 83.28 % 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 (0.24), residues: 1300 helix: 2.47 (0.19), residues: 758 sheet: -0.18 (0.38), residues: 160 loop : -0.60 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 490 HIS 0.003 0.001 HIS B 459 PHE 0.017 0.001 PHE B1124 TYR 0.017 0.001 TYR B1097 ARG 0.005 0.000 ARG A1112 *********************** 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 168 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.187 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 158 average time/residue: 0.1739 time to fit residues: 42.3102 Evaluate side-chains 151 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1002 time to fit residues: 4.2928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.0670 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10134 Z= 0.154 Angle : 0.455 7.531 13830 Z= 0.240 Chirality : 0.039 0.138 1636 Planarity : 0.003 0.027 1708 Dihedral : 11.254 173.028 1518 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.71 % Allowed : 15.54 % Favored : 82.74 % 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 (0.24), residues: 1300 helix: 2.56 (0.19), residues: 746 sheet: -0.15 (0.39), residues: 160 loop : -0.49 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 490 HIS 0.004 0.001 HIS B 459 PHE 0.012 0.001 PHE A1052 TYR 0.026 0.001 TYR A 519 ARG 0.002 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 164 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.090 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 159 average time/residue: 0.1621 time to fit residues: 40.6915 Evaluate side-chains 148 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0991 time to fit residues: 2.5355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 127 optimal weight: 0.0770 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10134 Z= 0.176 Angle : 0.456 6.643 13830 Z= 0.242 Chirality : 0.039 0.144 1636 Planarity : 0.003 0.027 1708 Dihedral : 9.960 135.351 1518 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.39 % Allowed : 16.51 % Favored : 82.10 % 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: 1.96 (0.24), residues: 1300 helix: 2.55 (0.19), residues: 746 sheet: -0.27 (0.39), residues: 162 loop : -0.46 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 490 HIS 0.004 0.001 HIS B 459 PHE 0.017 0.001 PHE A1124 TYR 0.014 0.001 TYR A 519 ARG 0.002 0.000 ARG A1112 *********************** 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 157 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 151 average time/residue: 0.1607 time to fit residues: 38.5091 Evaluate side-chains 147 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0976 time to fit residues: 3.6391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 0.0170 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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: 0.7977 moved from start: 0.3136 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= 0.139 Angle : 0.446 6.350 13830 Z= 0.234 Chirality : 0.038 0.158 1636 Planarity : 0.003 0.028 1708 Dihedral : 9.293 85.089 1518 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.96 % Allowed : 16.18 % Favored : 82.85 % 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: 2.63 (0.19), residues: 740 sheet: -0.25 (0.39), residues: 162 loop : -0.31 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 490 HIS 0.004 0.001 HIS A 774 PHE 0.014 0.001 PHE A 799 TYR 0.011 0.001 TYR B1097 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 158 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 153 average time/residue: 0.1608 time to fit residues: 39.0104 Evaluate side-chains 147 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0978 time to fit residues: 2.7665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 0.0970 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.3268 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= 0.143 Angle : 0.438 6.324 13830 Z= 0.233 Chirality : 0.038 0.176 1636 Planarity : 0.003 0.029 1708 Dihedral : 8.929 83.268 1518 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.64 % Allowed : 16.83 % Favored : 82.53 % 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: 2.09 (0.24), residues: 1300 helix: 2.63 (0.19), residues: 742 sheet: -0.25 (0.39), residues: 162 loop : -0.30 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 490 HIS 0.004 0.001 HIS B 774 PHE 0.020 0.001 PHE A1124 TYR 0.010 0.001 TYR B1097 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 150 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 146 average time/residue: 0.1727 time to fit residues: 40.3161 Evaluate side-chains 143 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1087 time to fit residues: 2.3677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 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 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10134 Z= 0.158 Angle : 0.448 6.472 13830 Z= 0.236 Chirality : 0.038 0.145 1636 Planarity : 0.003 0.028 1708 Dihedral : 8.650 76.422 1518 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.75 % Allowed : 17.47 % Favored : 81.78 % 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: 2.16 (0.24), residues: 1300 helix: 2.68 (0.19), residues: 740 sheet: -0.26 (0.39), residues: 162 loop : -0.22 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 490 HIS 0.004 0.001 HIS B 459 PHE 0.023 0.001 PHE B 799 TYR 0.011 0.001 TYR B1097 ARG 0.002 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 157 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 152 average time/residue: 0.1728 time to fit residues: 40.9866 Evaluate side-chains 147 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1021 time to fit residues: 2.7315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10134 Z= 0.218 Angle : 0.485 6.830 13830 Z= 0.255 Chirality : 0.039 0.158 1636 Planarity : 0.003 0.028 1708 Dihedral : 8.778 69.269 1518 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.64 % Allowed : 17.68 % Favored : 81.67 % 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: 2.10 (0.24), residues: 1300 helix: 2.62 (0.19), residues: 740 sheet: -0.36 (0.39), residues: 162 loop : -0.21 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 806 HIS 0.003 0.001 HIS A 459 PHE 0.015 0.001 PHE B 813 TYR 0.011 0.001 TYR B1097 ARG 0.003 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 148 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 1.140 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 145 average time/residue: 0.1691 time to fit residues: 38.3191 Evaluate side-chains 146 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1169 time to fit residues: 2.0611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.121534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095755 restraints weight = 19763.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099178 restraints weight = 9800.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101422 restraints weight = 6187.220| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3726 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= 0.128 Angle : 0.452 8.863 13830 Z= 0.233 Chirality : 0.038 0.140 1636 Planarity : 0.003 0.029 1708 Dihedral : 8.482 70.347 1518 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.75 % Allowed : 17.47 % Favored : 81.78 % 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: 2.18 (0.24), residues: 1300 helix: 2.67 (0.19), residues: 742 sheet: -0.27 (0.39), residues: 162 loop : -0.17 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 490 HIS 0.004 0.001 HIS B 459 PHE 0.015 0.001 PHE B 885 TYR 0.019 0.001 TYR A 519 ARG 0.005 0.000 ARG A1112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.38 seconds wall clock time: 35 minutes 5.39 seconds (2105.39 seconds total)