Starting phenix.real_space_refine on Sat Jul 20 09:43:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/07_2024/8k3x_36864_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/07_2024/8k3x_36864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/07_2024/8k3x_36864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/07_2024/8k3x_36864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/07_2024/8k3x_36864_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/07_2024/8k3x_36864_neut.cif" } resolution = 2.86 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= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 6738 2.51 5 N 1696 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 521": "OD1" <-> "OD2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 653": "OE1" <-> "OE2" 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 GLU 684": "OE1" <-> "OE2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 862": "OE1" <-> "OE2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "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 GLU 1000": "OE1" <-> "OE2" Residue "A TYR 1028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "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 TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 521": "OD1" <-> "OD2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 653": "OE1" <-> "OE2" 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 GLU 684": "OE1" <-> "OE2" Residue "B TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 862": "OE1" <-> "OE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 932": "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 GLU 1000": "OE1" <-> "OE2" Residue "B TYR 1028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "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: 10386 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5158 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 20, 'TRANS': 672} Chain breaks: 9 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 408 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 16, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 279 Chain: "B" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5158 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 20, 'TRANS': 672} Chain breaks: 9 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 408 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 16, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 279 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'BGI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'BGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.17, per 1000 atoms: 0.59 Number of scatterers: 10386 At special positions: 0 Unit cell: (77.38, 136.74, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1888 8.00 N 1696 7.00 C 6738 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: 4.20 Conformation dependent library (CDL) restraints added in 2.0 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 64.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.641A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.522A pdb=" N LYS A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 424 through 428 removed outlier: 4.020A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.590A pdb=" N LEU A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.543A pdb=" N LYS A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.687A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 4.072A pdb=" N ASN A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.536A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 3.734A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.704A pdb=" N PHE A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 3.613A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.756A 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 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 removed outlier: 3.950A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 4.380A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 3.906A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 784 through 807 Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.683A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.523A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 893 Processing helix chain 'A' and resid 917 through 932 Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.781A pdb=" N THR A 940 " --> pdb=" O TRP A 936 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 936 through 941' Processing helix chain 'A' and resid 941 through 948 removed outlier: 3.531A pdb=" N TYR A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 955 Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 997 through 1014 Processing helix chain 'A' and resid 1027 through 1045 removed outlier: 3.526A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1060 removed outlier: 3.811A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 3.523A pdb=" N THR A1075 " --> pdb=" O LYS A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1128 removed outlier: 4.241A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A1109 " --> pdb=" O VAL A1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.641A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.522A pdb=" N LYS B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 424 through 428 removed outlier: 4.020A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.591A pdb=" N LEU B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.543A pdb=" N LYS B 491 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.687A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 588 removed outlier: 4.073A pdb=" N ASN B 580 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.535A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 3.734A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.704A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 660 removed outlier: 3.613A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.755A 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 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 removed outlier: 3.950A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 4.381A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 3.906A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 784 through 807 Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.683A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 824 " --> pdb=" O THR B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.522A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 893 Processing helix chain 'B' and resid 917 through 932 Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.781A pdb=" N THR B 940 " --> pdb=" O TRP B 936 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 936 through 941' Processing helix chain 'B' and resid 941 through 948 removed outlier: 3.531A pdb=" N TYR B 945 " --> pdb=" O SER B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 955 Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 997 through 1014 Processing helix chain 'B' and resid 1027 through 1045 removed outlier: 3.525A pdb=" N SER B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1060 removed outlier: 3.811A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1075 removed outlier: 3.524A pdb=" N THR B1075 " --> pdb=" O LYS B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1128 removed outlier: 4.241A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER B1108 " --> pdb=" O LEU B1104 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B1109 " --> pdb=" O VAL B1105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 388 through 390 removed outlier: 6.164A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.927A pdb=" N THR A 453 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 629 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.818A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 388 through 390 removed outlier: 6.164A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.926A pdb=" N THR B 453 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 629 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.818A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1728 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: 3.18 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1634 1.30 - 1.43: 2967 1.43 - 1.55: 5921 1.55 - 1.68: 6 1.68 - 1.80: 96 Bond restraints: 10624 Sorted by residual: bond pdb=" C28 BGI A1201 " pdb=" N27 BGI A1201 " ideal model delta sigma weight residual 1.371 1.518 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C28 BGI B1201 " pdb=" N27 BGI B1201 " ideal model delta sigma weight residual 1.371 1.517 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" C28 BGI A1201 " pdb=" N22 BGI A1201 " ideal model delta sigma weight residual 1.382 1.515 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C28 BGI B1201 " pdb=" N22 BGI B1201 " ideal model delta sigma weight residual 1.382 1.514 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C13 BGI B1201 " pdb=" N15 BGI B1201 " ideal model delta sigma weight residual 1.343 1.472 -0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 10619 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.80: 172 105.80 - 112.86: 5750 112.86 - 119.92: 3729 119.92 - 126.97: 4723 126.97 - 134.03: 114 Bond angle restraints: 14488 Sorted by residual: angle pdb=" N LEU B 642 " pdb=" CA LEU B 642 " pdb=" C LEU B 642 " ideal model delta sigma weight residual 113.02 106.05 6.97 1.20e+00 6.94e-01 3.38e+01 angle pdb=" N LEU A 642 " pdb=" CA LEU A 642 " pdb=" C LEU A 642 " ideal model delta sigma weight residual 113.02 106.05 6.97 1.20e+00 6.94e-01 3.37e+01 angle pdb=" N THR B 422 " pdb=" CA THR B 422 " pdb=" C THR B 422 " ideal model delta sigma weight residual 114.56 107.87 6.69 1.27e+00 6.20e-01 2.78e+01 angle pdb=" N THR A 422 " pdb=" CA THR A 422 " pdb=" C THR A 422 " ideal model delta sigma weight residual 114.56 107.92 6.64 1.27e+00 6.20e-01 2.74e+01 angle pdb=" N TYR A 952 " pdb=" CA TYR A 952 " pdb=" C TYR A 952 " ideal model delta sigma weight residual 112.89 107.00 5.89 1.24e+00 6.50e-01 2.25e+01 ... (remaining 14483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 5702 15.94 - 31.88: 407 31.88 - 47.83: 85 47.83 - 63.77: 16 63.77 - 79.71: 16 Dihedral angle restraints: 6226 sinusoidal: 2144 harmonic: 4082 Sorted by residual: dihedral pdb=" CA ALA B 715 " pdb=" C ALA B 715 " pdb=" N GLU B 716 " pdb=" CA GLU B 716 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ALA A 715 " pdb=" C ALA A 715 " pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta harmonic sigma weight residual 180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA HIS B 828 " pdb=" C HIS B 828 " pdb=" N SER B 829 " pdb=" CA SER B 829 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1551 0.100 - 0.199: 135 0.199 - 0.299: 10 0.299 - 0.399: 0 0.399 - 0.498: 2 Chirality restraints: 1698 Sorted by residual: chirality pdb=" C19 BGI A1201 " pdb=" C18 BGI A1201 " pdb=" C20 BGI A1201 " pdb=" O30 BGI A1201 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" C19 BGI B1201 " pdb=" C18 BGI B1201 " pdb=" C20 BGI B1201 " pdb=" O30 BGI B1201 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA MET A 416 " pdb=" N MET A 416 " pdb=" C MET A 416 " pdb=" CB MET A 416 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1695 not shown) Planarity restraints: 1798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 539 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" C GLU A 539 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 539 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 540 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 539 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C GLU B 539 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU B 539 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS B 540 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1025 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO A1026 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A1026 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1026 " -0.031 5.00e-02 4.00e+02 ... (remaining 1795 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1319 2.74 - 3.28: 10267 3.28 - 3.82: 16541 3.82 - 4.36: 19582 4.36 - 4.90: 34528 Nonbonded interactions: 82237 Sorted by model distance: nonbonded pdb=" OD1 ASP B 602 " pdb=" O31 BGI B1201 " model vdw 2.196 2.440 nonbonded pdb=" OD2 ASP B 602 " pdb=" N15 BGI B1201 " model vdw 2.283 2.520 nonbonded pdb=" O ILE A 818 " pdb=" OG SER A 822 " model vdw 2.334 2.440 nonbonded pdb=" O ILE B 818 " pdb=" OG SER B 822 " model vdw 2.334 2.440 nonbonded pdb=" OG SER B 997 " pdb=" OE1 GLU B1000 " model vdw 2.371 2.440 ... (remaining 82232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.990 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.012 0.147 10624 Z= 0.762 Angle : 0.935 8.257 14488 Z= 0.580 Chirality : 0.061 0.498 1698 Planarity : 0.005 0.056 1798 Dihedral : 12.853 79.710 3582 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.20 % Allowed : 0.60 % Favored : 99.20 % 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: -0.82 (0.22), residues: 1346 helix: 0.48 (0.19), residues: 736 sheet: -2.28 (0.33), residues: 150 loop : -1.49 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 806 HIS 0.005 0.002 HIS B 965 PHE 0.021 0.002 PHE B 864 TYR 0.020 0.002 TYR A1008 ARG 0.005 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 1.081 Fit side-chains REVERT: A 458 ASP cc_start: 0.8416 (p0) cc_final: 0.7894 (p0) REVERT: A 466 LEU cc_start: 0.8415 (mt) cc_final: 0.8022 (mm) REVERT: A 514 SER cc_start: 0.8389 (t) cc_final: 0.8011 (p) REVERT: A 538 TYR cc_start: 0.7880 (m-80) cc_final: 0.7265 (m-80) REVERT: A 548 ASN cc_start: 0.7618 (t0) cc_final: 0.6465 (p0) REVERT: A 555 SER cc_start: 0.7594 (m) cc_final: 0.6852 (p) REVERT: A 653 GLU cc_start: 0.8261 (tt0) cc_final: 0.8031 (tt0) REVERT: A 745 ASP cc_start: 0.7872 (p0) cc_final: 0.7658 (p0) REVERT: A 766 PHE cc_start: 0.7460 (m-10) cc_final: 0.7021 (t80) REVERT: A 862 GLU cc_start: 0.8301 (tt0) cc_final: 0.8026 (tt0) REVERT: A 936 TRP cc_start: 0.7925 (m100) cc_final: 0.7704 (m100) REVERT: A 1067 TYR cc_start: 0.8317 (t80) cc_final: 0.7947 (t80) REVERT: A 1088 PRO cc_start: 0.8397 (Cg_endo) cc_final: 0.8177 (Cg_exo) REVERT: A 1103 TRP cc_start: 0.7698 (m100) cc_final: 0.7479 (m100) REVERT: B 428 LEU cc_start: 0.8171 (mm) cc_final: 0.7961 (mm) REVERT: B 433 PHE cc_start: 0.6810 (m-80) cc_final: 0.6371 (m-80) REVERT: B 466 LEU cc_start: 0.8343 (mt) cc_final: 0.8080 (mp) REVERT: B 471 ASP cc_start: 0.8134 (m-30) cc_final: 0.7597 (m-30) REVERT: B 514 SER cc_start: 0.8419 (t) cc_final: 0.7770 (p) REVERT: B 889 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7568 (mptt) REVERT: B 1114 ILE cc_start: 0.8393 (mt) cc_final: 0.8144 (mm) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.9766 time to fit residues: 243.6101 Evaluate side-chains 144 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 520 GLN A 614 GLN A 644 ASN A 828 HIS A 892 GLN A 977 ASN B 419 GLN B 828 HIS B 977 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10624 Z= 0.150 Angle : 0.475 6.465 14488 Z= 0.257 Chirality : 0.039 0.170 1698 Planarity : 0.004 0.064 1798 Dihedral : 5.112 31.644 1562 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.39 % Allowed : 9.64 % Favored : 87.97 % 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: 0.34 (0.23), residues: 1346 helix: 1.45 (0.19), residues: 770 sheet: -1.35 (0.38), residues: 144 loop : -1.43 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 584 HIS 0.007 0.001 HIS B 828 PHE 0.013 0.001 PHE B 766 TYR 0.019 0.001 TYR B 827 ARG 0.003 0.000 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8473 (mt) cc_final: 0.8241 (mm) REVERT: A 514 SER cc_start: 0.8547 (t) cc_final: 0.8284 (p) REVERT: A 548 ASN cc_start: 0.7887 (t0) cc_final: 0.6680 (p0) REVERT: A 555 SER cc_start: 0.7642 (m) cc_final: 0.6522 (p) REVERT: A 766 PHE cc_start: 0.7319 (m-10) cc_final: 0.6916 (t80) REVERT: A 977 ASN cc_start: 0.4695 (OUTLIER) cc_final: 0.3594 (t0) REVERT: A 1060 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: A 1067 TYR cc_start: 0.8399 (t80) cc_final: 0.8054 (t80) REVERT: A 1088 PRO cc_start: 0.8421 (Cg_endo) cc_final: 0.8192 (Cg_exo) REVERT: B 428 LEU cc_start: 0.8205 (mm) cc_final: 0.7980 (mm) REVERT: B 433 PHE cc_start: 0.6849 (m-80) cc_final: 0.6468 (m-80) REVERT: B 466 LEU cc_start: 0.8016 (mt) cc_final: 0.7766 (mm) REVERT: B 661 ASP cc_start: 0.7838 (m-30) cc_final: 0.7621 (m-30) REVERT: B 735 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8282 (ttmt) REVERT: B 977 ASN cc_start: 0.5052 (OUTLIER) cc_final: 0.4548 (t0) REVERT: B 1105 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7681 (p) outliers start: 24 outliers final: 9 residues processed: 187 average time/residue: 0.8382 time to fit residues: 174.1157 Evaluate side-chains 144 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 977 ASN Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 977 ASN Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS A 892 GLN A 977 ASN B 977 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10624 Z= 0.318 Angle : 0.523 6.203 14488 Z= 0.283 Chirality : 0.041 0.168 1698 Planarity : 0.004 0.055 1798 Dihedral : 5.385 41.546 1562 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.48 % Allowed : 12.62 % Favored : 83.90 % 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: 0.52 (0.23), residues: 1346 helix: 1.48 (0.19), residues: 786 sheet: -0.79 (0.39), residues: 142 loop : -1.42 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.008 0.002 HIS B 536 PHE 0.017 0.002 PHE B 766 TYR 0.021 0.002 TYR B 827 ARG 0.003 0.000 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8558 (mt) cc_final: 0.8343 (mm) REVERT: A 514 SER cc_start: 0.8661 (t) cc_final: 0.8364 (p) REVERT: A 548 ASN cc_start: 0.8330 (t0) cc_final: 0.7115 (p0) REVERT: A 555 SER cc_start: 0.7667 (m) cc_final: 0.6805 (p) REVERT: A 700 MET cc_start: 0.3857 (OUTLIER) cc_final: 0.3098 (tmt) REVERT: A 766 PHE cc_start: 0.7460 (m-10) cc_final: 0.7014 (t80) REVERT: A 1088 PRO cc_start: 0.8419 (Cg_endo) cc_final: 0.8129 (Cg_exo) REVERT: B 466 LEU cc_start: 0.8323 (mt) cc_final: 0.8067 (mm) REVERT: B 735 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8327 (ttmt) REVERT: B 784 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7490 (p0) REVERT: B 977 ASN cc_start: 0.4288 (OUTLIER) cc_final: 0.3641 (t0) REVERT: B 1067 TYR cc_start: 0.8489 (t80) cc_final: 0.8138 (t80) REVERT: B 1071 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7412 (mttm) outliers start: 35 outliers final: 15 residues processed: 139 average time/residue: 0.8486 time to fit residues: 131.0740 Evaluate side-chains 136 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 977 ASN Chi-restraints excluded: chain B residue 1071 LYS Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1117 SER Chi-restraints excluded: chain B residue 1120 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 0.0060 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 125 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 HIS A 856 ASN A 892 GLN B 977 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10624 Z= 0.233 Angle : 0.472 6.109 14488 Z= 0.255 Chirality : 0.040 0.166 1698 Planarity : 0.004 0.050 1798 Dihedral : 5.134 40.398 1562 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.68 % Allowed : 14.02 % Favored : 82.31 % 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: 0.88 (0.23), residues: 1346 helix: 1.80 (0.19), residues: 774 sheet: -0.49 (0.41), residues: 142 loop : -1.31 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 779 HIS 0.006 0.001 HIS B 536 PHE 0.018 0.001 PHE B 766 TYR 0.018 0.001 TYR B 827 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7874 (m-80) cc_final: 0.7560 (m-10) REVERT: A 466 LEU cc_start: 0.8561 (mt) cc_final: 0.8326 (mm) REVERT: A 514 SER cc_start: 0.8743 (t) cc_final: 0.8449 (p) REVERT: A 525 LYS cc_start: 0.7251 (mmtm) cc_final: 0.7020 (mmtt) REVERT: A 548 ASN cc_start: 0.8397 (t0) cc_final: 0.7264 (p0) REVERT: A 555 SER cc_start: 0.7849 (m) cc_final: 0.6730 (p) REVERT: A 689 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6684 (tm-30) REVERT: A 883 SER cc_start: 0.8637 (p) cc_final: 0.8423 (m) REVERT: A 892 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6597 (mt0) REVERT: A 1088 PRO cc_start: 0.8387 (Cg_endo) cc_final: 0.8082 (Cg_exo) REVERT: B 977 ASN cc_start: 0.3670 (OUTLIER) cc_final: 0.3076 (t0) REVERT: B 1067 TYR cc_start: 0.8517 (t80) cc_final: 0.8228 (t80) outliers start: 37 outliers final: 19 residues processed: 144 average time/residue: 0.8890 time to fit residues: 142.0722 Evaluate side-chains 141 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 977 ASN Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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 892 GLN A 965 HIS B 706 HIS B 977 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10624 Z= 0.310 Angle : 0.512 7.137 14488 Z= 0.273 Chirality : 0.041 0.167 1698 Planarity : 0.004 0.052 1798 Dihedral : 5.273 41.681 1562 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.27 % Allowed : 13.92 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1346 helix: 1.83 (0.19), residues: 766 sheet: -0.33 (0.41), residues: 142 loop : -1.32 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 936 HIS 0.006 0.002 HIS B 536 PHE 0.020 0.002 PHE B 766 TYR 0.018 0.001 TYR B 827 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 119 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 440 TYR cc_start: 0.8126 (m-80) cc_final: 0.7757 (m-10) REVERT: A 466 LEU cc_start: 0.8573 (mt) cc_final: 0.8339 (mm) REVERT: A 514 SER cc_start: 0.8932 (t) cc_final: 0.8658 (p) REVERT: A 548 ASN cc_start: 0.8486 (t0) cc_final: 0.7389 (p0) REVERT: A 555 SER cc_start: 0.7707 (m) cc_final: 0.6957 (p) REVERT: A 689 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: A 735 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8252 (mmmt) REVERT: A 1088 PRO cc_start: 0.8411 (Cg_endo) cc_final: 0.8086 (Cg_exo) REVERT: B 508 ARG cc_start: 0.7359 (mtp180) cc_final: 0.7088 (mmm-85) REVERT: B 553 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6378 (pp20) REVERT: B 784 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7544 (p0) REVERT: B 1067 TYR cc_start: 0.8557 (t80) cc_final: 0.8226 (t80) outliers start: 43 outliers final: 21 residues processed: 148 average time/residue: 0.9031 time to fit residues: 147.9796 Evaluate side-chains 141 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1117 SER Chi-restraints excluded: chain B residue 1120 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 133 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10624 Z= 0.224 Angle : 0.482 7.870 14488 Z= 0.255 Chirality : 0.040 0.168 1698 Planarity : 0.003 0.050 1798 Dihedral : 5.061 39.855 1562 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.27 % Allowed : 14.21 % Favored : 81.51 % 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: 1.10 (0.23), residues: 1346 helix: 1.97 (0.19), residues: 768 sheet: -0.12 (0.42), residues: 142 loop : -1.26 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 779 HIS 0.005 0.001 HIS B 536 PHE 0.018 0.001 PHE B 766 TYR 0.017 0.001 TYR B 827 ARG 0.002 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.094 Fit side-chains REVERT: A 440 TYR cc_start: 0.8106 (m-80) cc_final: 0.7697 (m-10) REVERT: A 466 LEU cc_start: 0.8572 (mt) cc_final: 0.8342 (mm) REVERT: A 514 SER cc_start: 0.8866 (t) cc_final: 0.8610 (p) REVERT: A 543 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6756 (mtp) REVERT: A 548 ASN cc_start: 0.8459 (t0) cc_final: 0.7804 (p0) REVERT: A 689 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 700 MET cc_start: 0.3947 (tmt) cc_final: 0.2697 (tpt) REVERT: A 735 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8250 (mmmt) REVERT: A 986 GLU cc_start: 0.5298 (OUTLIER) cc_final: 0.5033 (pp20) REVERT: A 1030 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6470 (tp30) REVERT: A 1088 PRO cc_start: 0.8325 (Cg_endo) cc_final: 0.8005 (Cg_exo) REVERT: B 508 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7212 (mmm-85) REVERT: B 516 LEU cc_start: 0.8230 (mm) cc_final: 0.8026 (mm) REVERT: B 553 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.6385 (pp20) REVERT: B 1067 TYR cc_start: 0.8575 (t80) cc_final: 0.8281 (t80) outliers start: 43 outliers final: 25 residues processed: 147 average time/residue: 0.9230 time to fit residues: 149.8020 Evaluate side-chains 144 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1117 SER Chi-restraints excluded: chain B residue 1120 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 892 GLN B 398 GLN B 965 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10624 Z= 0.159 Angle : 0.450 7.686 14488 Z= 0.239 Chirality : 0.039 0.165 1698 Planarity : 0.003 0.055 1798 Dihedral : 4.687 34.954 1562 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.68 % Allowed : 14.71 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1346 helix: 2.18 (0.19), residues: 766 sheet: 0.09 (0.43), residues: 142 loop : -1.16 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 779 HIS 0.004 0.001 HIS B 536 PHE 0.023 0.001 PHE B 881 TYR 0.017 0.001 TYR B 827 ARG 0.003 0.000 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7923 (m-80) cc_final: 0.7550 (m-10) REVERT: A 466 LEU cc_start: 0.8557 (mt) cc_final: 0.8310 (mm) REVERT: A 514 SER cc_start: 0.8861 (t) cc_final: 0.8605 (p) REVERT: A 543 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6763 (mtp) REVERT: A 548 ASN cc_start: 0.8425 (t0) cc_final: 0.7836 (p0) REVERT: A 689 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: A 700 MET cc_start: 0.3886 (tmt) cc_final: 0.2664 (tpt) REVERT: A 735 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8267 (mmmt) REVERT: A 986 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.5226 (pp20) REVERT: A 1088 PRO cc_start: 0.8241 (Cg_endo) cc_final: 0.7926 (Cg_exo) REVERT: B 516 LEU cc_start: 0.8241 (mm) cc_final: 0.7994 (mm) REVERT: B 1067 TYR cc_start: 0.8563 (t80) cc_final: 0.8300 (t80) outliers start: 37 outliers final: 18 residues processed: 145 average time/residue: 0.8570 time to fit residues: 138.0804 Evaluate side-chains 135 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 0.0060 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN B 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10624 Z= 0.245 Angle : 0.497 9.204 14488 Z= 0.262 Chirality : 0.040 0.162 1698 Planarity : 0.003 0.053 1798 Dihedral : 5.038 40.242 1562 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.08 % Allowed : 15.71 % Favored : 81.21 % 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: 1.30 (0.23), residues: 1346 helix: 2.09 (0.19), residues: 768 sheet: 0.07 (0.42), residues: 142 loop : -1.13 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 779 HIS 0.005 0.001 HIS A 536 PHE 0.019 0.001 PHE B 766 TYR 0.018 0.001 TYR B 827 ARG 0.002 0.000 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 440 TYR cc_start: 0.8224 (m-80) cc_final: 0.7815 (m-10) REVERT: A 466 LEU cc_start: 0.8584 (mt) cc_final: 0.8347 (mm) REVERT: A 514 SER cc_start: 0.8971 (t) cc_final: 0.8730 (p) REVERT: A 548 ASN cc_start: 0.8439 (t0) cc_final: 0.7954 (p0) REVERT: A 689 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.6684 (tm-30) REVERT: A 700 MET cc_start: 0.3899 (tmt) cc_final: 0.2679 (tpt) REVERT: A 735 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8171 (mmmt) REVERT: A 1030 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6483 (tp30) REVERT: A 1060 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: A 1088 PRO cc_start: 0.8298 (Cg_endo) cc_final: 0.7951 (Cg_exo) REVERT: B 684 GLU cc_start: 0.7377 (mp0) cc_final: 0.7168 (mp0) REVERT: B 1067 TYR cc_start: 0.8599 (t80) cc_final: 0.8292 (t80) outliers start: 31 outliers final: 21 residues processed: 138 average time/residue: 0.9065 time to fit residues: 138.2429 Evaluate side-chains 140 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1120 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10624 Z= 0.177 Angle : 0.460 8.937 14488 Z= 0.242 Chirality : 0.039 0.165 1698 Planarity : 0.003 0.052 1798 Dihedral : 4.744 36.178 1562 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.49 % Allowed : 16.70 % Favored : 80.82 % 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: 1.52 (0.23), residues: 1346 helix: 2.26 (0.18), residues: 766 sheet: 0.30 (0.42), residues: 142 loop : -1.07 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 779 HIS 0.004 0.001 HIS B 536 PHE 0.027 0.001 PHE B 881 TYR 0.017 0.001 TYR B 827 ARG 0.003 0.000 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 440 TYR cc_start: 0.8063 (m-80) cc_final: 0.7671 (m-10) REVERT: A 466 LEU cc_start: 0.8577 (mt) cc_final: 0.8321 (mm) REVERT: A 514 SER cc_start: 0.8996 (t) cc_final: 0.8756 (p) REVERT: A 548 ASN cc_start: 0.8435 (t0) cc_final: 0.7983 (p0) REVERT: A 689 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: A 700 MET cc_start: 0.3876 (tmt) cc_final: 0.2657 (tpt) REVERT: A 735 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8205 (mmmt) REVERT: A 1088 PRO cc_start: 0.8167 (Cg_endo) cc_final: 0.7871 (Cg_exo) REVERT: A 1120 MET cc_start: 0.8371 (tpt) cc_final: 0.8138 (tpp) REVERT: B 514 SER cc_start: 0.8704 (t) cc_final: 0.8390 (p) REVERT: B 684 GLU cc_start: 0.7387 (mp0) cc_final: 0.7185 (mp0) REVERT: B 1067 TYR cc_start: 0.8614 (t80) cc_final: 0.8351 (t80) outliers start: 25 outliers final: 17 residues processed: 136 average time/residue: 0.8762 time to fit residues: 132.3077 Evaluate side-chains 132 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10624 Z= 0.127 Angle : 0.442 9.898 14488 Z= 0.230 Chirality : 0.039 0.214 1698 Planarity : 0.003 0.049 1798 Dihedral : 4.369 30.767 1562 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.99 % Allowed : 17.40 % Favored : 80.62 % 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: 1.69 (0.23), residues: 1346 helix: 2.37 (0.19), residues: 778 sheet: 0.52 (0.43), residues: 142 loop : -1.10 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 806 HIS 0.004 0.001 HIS B 536 PHE 0.017 0.001 PHE B 766 TYR 0.022 0.001 TYR A1067 ARG 0.004 0.000 ARG A 759 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.139 Fit side-chains REVERT: A 440 TYR cc_start: 0.7944 (m-80) cc_final: 0.7566 (m-10) REVERT: A 466 LEU cc_start: 0.8561 (mt) cc_final: 0.8282 (mm) REVERT: A 514 SER cc_start: 0.8893 (t) cc_final: 0.8652 (p) REVERT: A 548 ASN cc_start: 0.8449 (t0) cc_final: 0.8045 (p0) REVERT: A 700 MET cc_start: 0.3819 (tmt) cc_final: 0.2653 (tpt) REVERT: A 735 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8226 (mmmt) REVERT: A 1060 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: A 1088 PRO cc_start: 0.8058 (Cg_endo) cc_final: 0.7725 (Cg_exo) REVERT: A 1120 MET cc_start: 0.8245 (tpt) cc_final: 0.8030 (tpp) REVERT: B 514 SER cc_start: 0.8697 (t) cc_final: 0.8399 (p) REVERT: B 684 GLU cc_start: 0.7403 (mp0) cc_final: 0.7192 (mp0) REVERT: B 1067 TYR cc_start: 0.8539 (t80) cc_final: 0.8261 (t80) outliers start: 20 outliers final: 16 residues processed: 133 average time/residue: 0.9250 time to fit residues: 136.4076 Evaluate side-chains 131 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 0.0980 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116485 restraints weight = 12591.821| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.02 r_work: 0.3271 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10624 Z= 0.168 Angle : 0.457 8.837 14488 Z= 0.238 Chirality : 0.039 0.235 1698 Planarity : 0.003 0.050 1798 Dihedral : 4.549 35.182 1562 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.09 % Allowed : 17.20 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1346 helix: 2.35 (0.18), residues: 778 sheet: 0.56 (0.44), residues: 142 loop : -1.05 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 806 HIS 0.005 0.001 HIS A 536 PHE 0.028 0.001 PHE B 881 TYR 0.016 0.001 TYR B 827 ARG 0.004 0.000 ARG A 759 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.86 seconds wall clock time: 58 minutes 55.67 seconds (3535.67 seconds total)