Starting phenix.real_space_refine on Sat Jul 20 04:01:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/07_2024/8k3t_36859_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/07_2024/8k3t_36859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/07_2024/8k3t_36859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/07_2024/8k3t_36859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/07_2024/8k3t_36859_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/07_2024/8k3t_36859_neut.cif" } resolution = 3.57 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= 0.004 sd= 0.052 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 6178 2.51 5 N 1482 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 925": "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 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1060": "OE1" <-> "OE2" Residue "A TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 526": "OD1" <-> "OD2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 794": "OE1" <-> "OE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 925": "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 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1060": "OE1" <-> "OE2" Residue "B TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4630 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 283 Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4630 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 283 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.56, per 1000 atoms: 0.59 Number of scatterers: 9410 At special positions: 0 Unit cell: (113.42, 109.18, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 4 11.99 O 1682 8.00 N 1482 7.00 C 6178 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: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 67.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.876A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.538A pdb=" N TYR A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 478 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 516 removed outlier: 4.155A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.617A pdb=" N ARG A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 Processing helix chain 'A' and resid 610 through 618 removed outlier: 3.817A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 3.927A pdb=" N PHE A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 643 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 669 removed outlier: 3.539A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.748A pdb=" N GLY A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 715 through 726 removed outlier: 4.470A pdb=" N LEU A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.627A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.602A pdb=" N TRP A 779 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.829A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 861 through 893 removed outlier: 3.776A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 933 Processing helix chain 'A' and resid 942 through 955 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 1027 through 1060 removed outlier: 4.176A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1091 through 1130 removed outlier: 4.073A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.875A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.538A pdb=" N TYR B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 516 removed outlier: 4.154A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.615A pdb=" N ARG B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 610 through 618 removed outlier: 3.818A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.927A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 643 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 669 removed outlier: 3.540A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.749A pdb=" N GLY B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 715 through 726 removed outlier: 4.470A pdb=" N LEU B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.626A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.603A pdb=" N TRP B 779 " --> pdb=" O TYR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 Processing helix chain 'B' and resid 807 through 828 Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.829A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 861 through 893 removed outlier: 3.776A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 933 Processing helix chain 'B' and resid 942 through 955 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 1027 through 1060 removed outlier: 4.176A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1091 through 1130 removed outlier: 4.071A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 417 through 421 removed outlier: 3.683A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 493 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU A 568 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 495 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 629 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.770A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.682A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 493 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU B 568 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 495 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET B 449 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B 601 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 451 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY B 629 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 549 removed outlier: 4.769A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1803 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: 3.02 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1629 1.32 - 1.45: 2673 1.45 - 1.57: 5244 1.57 - 1.69: 10 1.69 - 1.81: 86 Bond restraints: 9642 Sorted by residual: bond pdb=" O1A UDP B1502 " pdb=" PA UDP B1502 " ideal model delta sigma weight residual 1.482 1.527 -0.045 1.00e-02 1.00e+04 1.99e+01 bond pdb=" O1A UDP A1502 " pdb=" PA UDP A1502 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.92e+01 bond pdb=" N ILE A 493 " pdb=" CA ILE A 493 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N VAL B 533 " pdb=" CA VAL B 533 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.15e-02 7.56e+03 9.53e+00 bond pdb=" N ILE B 493 " pdb=" CA ILE B 493 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.37e+00 ... (remaining 9637 not shown) Histogram of bond angle deviations from ideal: 97.39 - 104.77: 130 104.77 - 112.15: 4981 112.15 - 119.54: 3164 119.54 - 126.92: 4794 126.92 - 134.30: 103 Bond angle restraints: 13172 Sorted by residual: angle pdb=" CA PHE B 831 " pdb=" C PHE B 831 " pdb=" N ASN B 832 " ideal model delta sigma weight residual 118.27 108.41 9.86 1.59e+00 3.96e-01 3.84e+01 angle pdb=" CA PHE A 831 " pdb=" C PHE A 831 " pdb=" N ASN A 832 " ideal model delta sigma weight residual 118.27 108.42 9.85 1.59e+00 3.96e-01 3.84e+01 angle pdb=" O5' UDP A1502 " pdb=" PA UDP A1502 " pdb=" O1A UDP A1502 " ideal model delta sigma weight residual 106.70 111.20 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" O5' UDP B1502 " pdb=" PA UDP B1502 " pdb=" O1A UDP B1502 " ideal model delta sigma weight residual 106.70 111.18 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" O2A UDP B1502 " pdb=" PA UDP B1502 " pdb=" O3A UDP B1502 " ideal model delta sigma weight residual 105.97 110.25 -4.28 1.00e+00 1.00e+00 1.83e+01 ... (remaining 13167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 5282 23.20 - 46.40: 230 46.40 - 69.59: 42 69.59 - 92.79: 24 92.79 - 115.99: 2 Dihedral angle restraints: 5580 sinusoidal: 1878 harmonic: 3702 Sorted by residual: dihedral pdb=" C27 POV B1503 " pdb=" C28 POV B1503 " pdb=" C29 POV B1503 " pdb="C210 POV B1503 " ideal model delta sinusoidal sigma weight residual 127.48 -116.53 -115.99 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C27 POV A1503 " pdb=" C28 POV A1503 " pdb=" C29 POV A1503 " pdb="C210 POV A1503 " ideal model delta sinusoidal sigma weight residual 127.48 -116.59 -115.93 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CA PHE A 911 " pdb=" C PHE A 911 " pdb=" N ARG A 912 " pdb=" CA ARG A 912 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 939 0.041 - 0.082: 444 0.082 - 0.124: 128 0.124 - 0.165: 29 0.165 - 0.206: 10 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA ILE B 719 " pdb=" N ILE B 719 " pdb=" C ILE B 719 " pdb=" CB ILE B 719 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 719 " pdb=" N ILE A 719 " pdb=" C ILE A 719 " pdb=" CB ILE A 719 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL A 421 " pdb=" N VAL A 421 " pdb=" C VAL A 421 " pdb=" CB VAL A 421 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1547 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1503 " -0.025 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" C29 POV A1503 " 0.059 2.00e-02 2.50e+03 pdb="C210 POV A1503 " -0.059 2.00e-02 2.50e+03 pdb="C211 POV A1503 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1503 " 0.025 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C29 POV B1503 " -0.059 2.00e-02 2.50e+03 pdb="C210 POV B1503 " 0.059 2.00e-02 2.50e+03 pdb="C211 POV B1503 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 606 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 607 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " 0.026 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1967 2.76 - 3.30: 10068 3.30 - 3.83: 15870 3.83 - 4.36: 17632 4.36 - 4.90: 29939 Nonbonded interactions: 75476 Sorted by model distance: nonbonded pdb=" O ALA A 511 " pdb=" OG SER A 515 " model vdw 2.225 2.440 nonbonded pdb=" O ALA B 511 " pdb=" OG SER B 515 " model vdw 2.225 2.440 nonbonded pdb=" OE2 GLU A1060 " pdb=" OG1 THR A1091 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU B1060 " pdb=" OG1 THR B1091 " model vdw 2.263 2.440 nonbonded pdb=" O1A UDP B1502 " pdb="MG MG B1504 " model vdw 2.287 2.170 ... (remaining 75471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.650 Find NCS groups from input model: 0.360 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.009 0.081 9642 Z= 0.605 Angle : 0.929 10.229 13172 Z= 0.555 Chirality : 0.052 0.206 1550 Planarity : 0.005 0.047 1612 Dihedral : 15.004 115.988 3184 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.12 % Allowed : 1.34 % Favored : 97.54 % 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: 0.41 (0.25), residues: 1234 helix: 1.11 (0.20), residues: 672 sheet: -0.96 (0.44), residues: 154 loop : -0.47 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 806 HIS 0.006 0.002 HIS B 783 PHE 0.021 0.002 PHE A1052 TYR 0.028 0.002 TYR B 878 ARG 0.004 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASN cc_start: 0.3025 (OUTLIER) cc_final: 0.2570 (p0) REVERT: A 437 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8097 (mm110) REVERT: A 560 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8429 (tp40) REVERT: A 568 LEU cc_start: 0.7665 (tt) cc_final: 0.7193 (mp) REVERT: A 823 ILE cc_start: 0.9063 (tt) cc_final: 0.8791 (tt) REVERT: A 886 MET cc_start: 0.8323 (mtt) cc_final: 0.7679 (tmm) REVERT: B 411 ASN cc_start: 0.3117 (OUTLIER) cc_final: 0.2657 (p0) REVERT: B 437 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8137 (mm110) REVERT: B 560 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8454 (tp40) REVERT: B 568 LEU cc_start: 0.7621 (tt) cc_final: 0.7191 (mp) REVERT: B 823 ILE cc_start: 0.9066 (tt) cc_final: 0.8786 (tt) REVERT: B 886 MET cc_start: 0.8316 (mtt) cc_final: 0.7693 (tmm) outliers start: 10 outliers final: 0 residues processed: 157 average time/residue: 0.1768 time to fit residues: 40.8224 Evaluate side-chains 111 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain B residue 411 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 774 HIS B 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9642 Z= 0.182 Angle : 0.541 6.980 13172 Z= 0.293 Chirality : 0.040 0.150 1550 Planarity : 0.003 0.037 1612 Dihedral : 12.708 119.304 1474 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.12 % Allowed : 6.26 % Favored : 92.62 % 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: 1.26 (0.25), residues: 1234 helix: 1.77 (0.19), residues: 742 sheet: -0.44 (0.45), residues: 152 loop : -0.56 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1103 HIS 0.004 0.001 HIS A 828 PHE 0.017 0.001 PHE B 864 TYR 0.015 0.002 TYR A 713 ARG 0.003 0.001 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.036 Fit side-chains REVERT: A 560 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8422 (tp40) REVERT: A 823 ILE cc_start: 0.9072 (tt) cc_final: 0.8872 (tt) REVERT: A 879 MET cc_start: 0.8443 (ttp) cc_final: 0.8155 (ttp) REVERT: A 938 MET cc_start: 0.8605 (tpp) cc_final: 0.8392 (tpp) REVERT: B 560 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8440 (tp40) REVERT: B 568 LEU cc_start: 0.7581 (tt) cc_final: 0.7184 (mp) REVERT: B 879 MET cc_start: 0.8440 (ttp) cc_final: 0.8154 (ttp) REVERT: B 938 MET cc_start: 0.8609 (tpp) cc_final: 0.8367 (tpp) outliers start: 10 outliers final: 8 residues processed: 148 average time/residue: 0.1526 time to fit residues: 35.3524 Evaluate side-chains 120 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 0.0270 chunk 90 optimal weight: 10.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS B 582 HIS B 774 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9642 Z= 0.303 Angle : 0.568 6.138 13172 Z= 0.305 Chirality : 0.042 0.166 1550 Planarity : 0.003 0.040 1612 Dihedral : 13.285 137.003 1470 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.24 % Allowed : 12.08 % Favored : 85.68 % 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: 1.48 (0.25), residues: 1234 helix: 1.97 (0.19), residues: 740 sheet: -0.21 (0.46), residues: 152 loop : -0.60 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 806 HIS 0.003 0.001 HIS A 828 PHE 0.023 0.002 PHE A1052 TYR 0.012 0.002 TYR B 713 ARG 0.004 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 HIS cc_start: 0.7561 (p-80) cc_final: 0.6766 (p-80) REVERT: A 560 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8458 (tp40) REVERT: A 938 MET cc_start: 0.8729 (tpp) cc_final: 0.8203 (tpp) REVERT: A 1066 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8269 (t70) REVERT: B 459 HIS cc_start: 0.7590 (p-80) cc_final: 0.6840 (p-80) REVERT: B 560 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8432 (tp40) REVERT: B 568 LEU cc_start: 0.7738 (tt) cc_final: 0.7284 (mp) REVERT: B 1066 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8250 (t70) outliers start: 20 outliers final: 14 residues processed: 127 average time/residue: 0.1610 time to fit residues: 32.8558 Evaluate side-chains 126 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 0.0970 chunk 75 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9642 Z= 0.149 Angle : 0.467 5.850 13172 Z= 0.250 Chirality : 0.040 0.197 1550 Planarity : 0.003 0.034 1612 Dihedral : 12.891 137.884 1470 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.57 % Allowed : 13.20 % Favored : 84.23 % 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: 1.80 (0.25), residues: 1234 helix: 2.34 (0.19), residues: 740 sheet: -0.20 (0.45), residues: 152 loop : -0.72 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 PHE 0.013 0.001 PHE A 864 TYR 0.012 0.001 TYR B 713 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7212 (tp-100) REVERT: A 459 HIS cc_start: 0.7537 (p-80) cc_final: 0.6874 (p90) REVERT: A 519 TYR cc_start: 0.8129 (t80) cc_final: 0.7895 (t80) REVERT: A 560 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8444 (tp40) REVERT: A 810 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8735 (m) REVERT: A 876 MET cc_start: 0.8982 (tpp) cc_final: 0.8592 (tpp) REVERT: A 1052 PHE cc_start: 0.8618 (t80) cc_final: 0.8221 (t80) REVERT: A 1066 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8120 (t70) REVERT: B 437 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7330 (tp-100) REVERT: B 459 HIS cc_start: 0.7598 (p-80) cc_final: 0.6904 (p90) REVERT: B 560 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8440 (tp40) REVERT: B 810 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8749 (m) REVERT: B 876 MET cc_start: 0.8980 (tpp) cc_final: 0.8597 (tpp) REVERT: B 938 MET cc_start: 0.8547 (tpp) cc_final: 0.7692 (tpp) REVERT: B 1052 PHE cc_start: 0.8615 (t80) cc_final: 0.8219 (t80) outliers start: 23 outliers final: 13 residues processed: 131 average time/residue: 0.1534 time to fit residues: 31.6202 Evaluate side-chains 130 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9642 Z= 0.226 Angle : 0.498 6.341 13172 Z= 0.267 Chirality : 0.040 0.199 1550 Planarity : 0.003 0.035 1612 Dihedral : 12.902 139.650 1470 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.91 % Allowed : 14.88 % Favored : 82.21 % 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: 1.86 (0.25), residues: 1234 helix: 2.38 (0.19), residues: 740 sheet: -0.10 (0.46), residues: 152 loop : -0.73 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.003 0.001 HIS B 828 PHE 0.019 0.001 PHE B1052 TYR 0.010 0.001 TYR A 878 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.024 Fit side-chains REVERT: A 437 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7150 (tp-100) REVERT: A 560 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8480 (tp40) REVERT: A 886 MET cc_start: 0.7911 (ttp) cc_final: 0.7520 (tmm) REVERT: A 1066 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8165 (t70) REVERT: B 437 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7209 (tp-100) REVERT: B 543 MET cc_start: 0.6952 (pmm) cc_final: 0.6639 (ptp) REVERT: B 560 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8446 (tp40) REVERT: B 568 LEU cc_start: 0.7764 (tt) cc_final: 0.7312 (mp) REVERT: B 886 MET cc_start: 0.7956 (ttp) cc_final: 0.7635 (tmm) outliers start: 26 outliers final: 19 residues processed: 124 average time/residue: 0.1489 time to fit residues: 29.0280 Evaluate side-chains 131 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 0.0670 chunk 119 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9642 Z= 0.159 Angle : 0.479 6.244 13172 Z= 0.253 Chirality : 0.039 0.197 1550 Planarity : 0.003 0.034 1612 Dihedral : 12.657 140.221 1470 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.02 % Allowed : 16.11 % Favored : 80.87 % 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: 1.98 (0.25), residues: 1234 helix: 2.51 (0.19), residues: 740 sheet: -0.07 (0.46), residues: 152 loop : -0.73 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.003 0.001 HIS A 828 PHE 0.019 0.001 PHE A 772 TYR 0.009 0.001 TYR B 713 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.948 Fit side-chains REVERT: A 437 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7154 (tp-100) REVERT: A 476 MET cc_start: 0.8396 (mpp) cc_final: 0.7335 (mpp) REVERT: A 560 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8473 (tp40) REVERT: A 810 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8754 (m) REVERT: A 876 MET cc_start: 0.9031 (tpp) cc_final: 0.8779 (tpp) REVERT: A 886 MET cc_start: 0.7986 (ttp) cc_final: 0.7604 (tmm) REVERT: A 925 TYR cc_start: 0.8158 (m-10) cc_final: 0.7869 (m-80) REVERT: A 938 MET cc_start: 0.8521 (tpp) cc_final: 0.7569 (tpp) REVERT: A 1052 PHE cc_start: 0.8650 (t80) cc_final: 0.8268 (t80) REVERT: A 1066 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8211 (t70) REVERT: B 437 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7164 (tp-100) REVERT: B 476 MET cc_start: 0.8427 (mpp) cc_final: 0.7603 (mpp) REVERT: B 560 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8489 (tp40) REVERT: B 810 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8756 (m) REVERT: B 876 MET cc_start: 0.9029 (tpp) cc_final: 0.8781 (tpp) REVERT: B 886 MET cc_start: 0.7994 (ttp) cc_final: 0.7609 (tmm) REVERT: B 925 TYR cc_start: 0.8087 (m-10) cc_final: 0.7780 (m-80) REVERT: B 938 MET cc_start: 0.8456 (tpp) cc_final: 0.7532 (tpp) REVERT: B 1052 PHE cc_start: 0.8611 (t80) cc_final: 0.8210 (t80) outliers start: 27 outliers final: 19 residues processed: 136 average time/residue: 0.1597 time to fit residues: 33.5689 Evaluate side-chains 140 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9642 Z= 0.239 Angle : 0.517 7.489 13172 Z= 0.274 Chirality : 0.040 0.186 1550 Planarity : 0.003 0.034 1612 Dihedral : 12.551 140.997 1470 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.80 % Allowed : 17.00 % Favored : 80.20 % 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: 1.86 (0.25), residues: 1234 helix: 2.33 (0.19), residues: 756 sheet: -0.17 (0.46), residues: 152 loop : -0.70 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 806 HIS 0.002 0.001 HIS B 706 PHE 0.021 0.001 PHE B1052 TYR 0.019 0.001 TYR A 455 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.148 Fit side-chains REVERT: A 437 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7177 (tp-100) REVERT: A 476 MET cc_start: 0.8381 (mpp) cc_final: 0.8089 (mpp) REVERT: A 543 MET cc_start: 0.7008 (pmm) cc_final: 0.6710 (ptp) REVERT: A 560 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8446 (tp40) REVERT: A 606 MET cc_start: 0.6115 (mtm) cc_final: 0.5396 (mtt) REVERT: A 876 MET cc_start: 0.8952 (tpp) cc_final: 0.8546 (tpp) REVERT: A 886 MET cc_start: 0.8076 (ttp) cc_final: 0.7650 (tmm) REVERT: A 925 TYR cc_start: 0.8185 (m-10) cc_final: 0.7900 (m-80) REVERT: A 938 MET cc_start: 0.8595 (tpp) cc_final: 0.7656 (tpp) REVERT: A 1066 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8302 (t70) REVERT: B 437 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7161 (tp-100) REVERT: B 476 MET cc_start: 0.8380 (mpp) cc_final: 0.7413 (mpp) REVERT: B 543 MET cc_start: 0.6910 (pmm) cc_final: 0.6704 (ptp) REVERT: B 560 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8465 (tp40) REVERT: B 606 MET cc_start: 0.6089 (mtm) cc_final: 0.5350 (mtt) REVERT: B 876 MET cc_start: 0.8952 (tpp) cc_final: 0.8546 (tpp) REVERT: B 886 MET cc_start: 0.8085 (ttp) cc_final: 0.7690 (tmm) REVERT: B 925 TYR cc_start: 0.8113 (m-10) cc_final: 0.7815 (m-80) REVERT: B 938 MET cc_start: 0.8601 (tpp) cc_final: 0.7671 (tpp) outliers start: 25 outliers final: 23 residues processed: 127 average time/residue: 0.1555 time to fit residues: 30.7602 Evaluate side-chains 138 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9642 Z= 0.262 Angle : 0.535 6.243 13172 Z= 0.285 Chirality : 0.040 0.189 1550 Planarity : 0.003 0.035 1612 Dihedral : 12.391 141.465 1470 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.47 % Allowed : 17.00 % 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: 1.79 (0.25), residues: 1234 helix: 2.31 (0.19), residues: 746 sheet: -0.22 (0.46), residues: 152 loop : -0.71 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.002 0.001 HIS A 937 PHE 0.021 0.001 PHE A1052 TYR 0.013 0.001 TYR A 455 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 1.124 Fit side-chains REVERT: A 437 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7183 (tp-100) REVERT: A 476 MET cc_start: 0.8372 (mpp) cc_final: 0.7244 (mpp) REVERT: A 543 MET cc_start: 0.6930 (pmm) cc_final: 0.6698 (ptp) REVERT: A 606 MET cc_start: 0.6072 (mtm) cc_final: 0.5361 (mtt) REVERT: A 810 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8777 (m) REVERT: A 886 MET cc_start: 0.8107 (ttp) cc_final: 0.7594 (tmm) REVERT: A 925 TYR cc_start: 0.8207 (m-10) cc_final: 0.7899 (m-80) REVERT: A 938 MET cc_start: 0.8656 (tpp) cc_final: 0.7665 (tpp) REVERT: B 437 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7143 (tp-100) REVERT: B 476 MET cc_start: 0.8399 (mpp) cc_final: 0.8017 (mpp) REVERT: B 560 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8473 (tp40) REVERT: B 606 MET cc_start: 0.6178 (mtm) cc_final: 0.5455 (mtt) REVERT: B 810 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8771 (m) REVERT: B 925 TYR cc_start: 0.8130 (m-10) cc_final: 0.7828 (m-80) REVERT: B 938 MET cc_start: 0.8639 (tpp) cc_final: 0.7688 (tpp) outliers start: 31 outliers final: 26 residues processed: 125 average time/residue: 0.1633 time to fit residues: 31.3572 Evaluate side-chains 138 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 0.0770 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9642 Z= 0.142 Angle : 0.507 10.231 13172 Z= 0.262 Chirality : 0.040 0.182 1550 Planarity : 0.003 0.035 1612 Dihedral : 11.716 138.191 1470 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.91 % Allowed : 18.23 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.25), residues: 1234 helix: 2.45 (0.19), residues: 746 sheet: -0.19 (0.46), residues: 152 loop : -0.65 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.003 0.001 HIS A 828 PHE 0.018 0.001 PHE B 772 TYR 0.015 0.001 TYR A 455 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.078 Fit side-chains REVERT: A 437 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7161 (tp-100) REVERT: A 476 MET cc_start: 0.8477 (mpp) cc_final: 0.8128 (mpp) REVERT: A 606 MET cc_start: 0.5989 (mtm) cc_final: 0.5304 (mtt) REVERT: A 886 MET cc_start: 0.8115 (ttp) cc_final: 0.7636 (tmm) REVERT: A 925 TYR cc_start: 0.8157 (m-10) cc_final: 0.7862 (m-80) REVERT: A 938 MET cc_start: 0.8625 (tpp) cc_final: 0.7633 (tpp) REVERT: A 1052 PHE cc_start: 0.8635 (t80) cc_final: 0.8190 (t80) REVERT: B 416 MET cc_start: 0.6665 (tmm) cc_final: 0.5627 (ttt) REVERT: B 437 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7186 (tp-100) REVERT: B 476 MET cc_start: 0.8411 (mpp) cc_final: 0.7329 (mpp) REVERT: B 560 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8436 (tp40) REVERT: B 886 MET cc_start: 0.7739 (tmm) cc_final: 0.7298 (tmm) REVERT: B 925 TYR cc_start: 0.8127 (m-10) cc_final: 0.7830 (m-80) REVERT: B 938 MET cc_start: 0.8617 (tpp) cc_final: 0.7638 (tpp) REVERT: B 1052 PHE cc_start: 0.8638 (t80) cc_final: 0.8184 (t80) outliers start: 26 outliers final: 24 residues processed: 131 average time/residue: 0.1624 time to fit residues: 32.7275 Evaluate side-chains 140 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9642 Z= 0.231 Angle : 0.524 7.280 13172 Z= 0.274 Chirality : 0.040 0.186 1550 Planarity : 0.003 0.036 1612 Dihedral : 11.132 133.343 1470 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.57 % Allowed : 18.57 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1234 helix: 2.38 (0.19), residues: 746 sheet: -0.23 (0.45), residues: 152 loop : -0.69 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 806 HIS 0.002 0.001 HIS A 937 PHE 0.023 0.001 PHE B1052 TYR 0.011 0.001 TYR A 455 ARG 0.003 0.000 ARG A 758 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.079 Fit side-chains REVERT: A 437 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7174 (tp-100) REVERT: A 476 MET cc_start: 0.8422 (mpp) cc_final: 0.8054 (mpp) REVERT: A 543 MET cc_start: 0.6885 (pmm) cc_final: 0.6626 (ptp) REVERT: A 606 MET cc_start: 0.5994 (mtm) cc_final: 0.5312 (mtt) REVERT: A 886 MET cc_start: 0.8059 (ttp) cc_final: 0.7830 (tmm) REVERT: A 925 TYR cc_start: 0.8188 (m-10) cc_final: 0.7888 (m-80) REVERT: A 938 MET cc_start: 0.8664 (tpp) cc_final: 0.7665 (tpp) REVERT: B 416 MET cc_start: 0.6845 (tmm) cc_final: 0.5325 (ttt) REVERT: B 437 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7206 (tp-100) REVERT: B 606 MET cc_start: 0.6041 (mtm) cc_final: 0.5340 (mtt) REVERT: B 832 ASN cc_start: 0.7035 (p0) cc_final: 0.6706 (p0) REVERT: B 886 MET cc_start: 0.7761 (tmm) cc_final: 0.7417 (tmm) REVERT: B 925 TYR cc_start: 0.8113 (m-10) cc_final: 0.7807 (m-80) REVERT: B 938 MET cc_start: 0.8649 (tpp) cc_final: 0.7693 (tpp) outliers start: 23 outliers final: 20 residues processed: 118 average time/residue: 0.1582 time to fit residues: 29.0499 Evaluate side-chains 129 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 0.0170 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 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 = 0.3948 r_free = 0.3948 target = 0.126159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.093246 restraints weight = 20625.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.096608 restraints weight = 9210.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098694 restraints weight = 5715.991| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9642 Z= 0.163 Angle : 0.497 7.666 13172 Z= 0.256 Chirality : 0.039 0.178 1550 Planarity : 0.003 0.036 1612 Dihedral : 10.807 130.062 1470 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.57 % Allowed : 18.90 % Favored : 78.52 % 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: 1.98 (0.25), residues: 1234 helix: 2.47 (0.19), residues: 744 sheet: -0.15 (0.45), residues: 152 loop : -0.65 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.002 0.001 HIS A 828 PHE 0.017 0.001 PHE B 772 TYR 0.014 0.001 TYR A 455 ARG 0.002 0.000 ARG A 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1673.20 seconds wall clock time: 31 minutes 0.59 seconds (1860.59 seconds total)