Starting phenix.real_space_refine on Sat Dec 9 07:19:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/12_2023/8k3x_36864_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/12_2023/8k3x_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_36864/12_2023/8k3x_36864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/12_2023/8k3x_36864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/12_2023/8k3x_36864_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3x_36864/12_2023/8k3x_36864_neut_updated.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.05, per 1000 atoms: 0.58 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: 4.34 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... running ksdssp... Secondary structure from input PDB file: 62 helices and 8 sheets defined 56.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.641A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 459 through 478 removed outlier: 5.130A pdb=" N MET A 470 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASP A 471 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN A 472 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL A 473 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 507 through 516 removed outlier: 3.687A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.687A pdb=" N SER A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 611 through 620 removed outlier: 3.612A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 620 " --> pdb=" O TRP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 645 through 659 removed outlier: 3.613A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 668 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 686 No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 707 through 714 removed outlier: 5.437A pdb=" N TYR A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 725 removed outlier: 3.703A pdb=" N ILE A 719 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 720 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 721 " --> pdb=" O ARG A 718 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 725 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 773 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 780 Processing helix chain 'A' and resid 785 through 806 Processing helix chain 'A' and resid 808 through 827 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 831 through 855 Processing helix chain 'A' and resid 863 through 892 Processing helix chain 'A' and resid 918 through 931 Processing helix chain 'A' and resid 936 through 940 removed outlier: 4.102A pdb=" N LEU A 939 " --> pdb=" O TRP A 936 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 940 " --> pdb=" O HIS A 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 936 through 940' Processing helix chain 'A' and resid 942 through 947 Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 956 through 963 Processing helix chain 'A' and resid 998 through 1014 Processing helix chain 'A' and resid 1028 through 1059 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) removed outlier: 5.046A pdb=" N TRP A1047 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A1048 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE A1049 " --> pdb=" O ILE A1044 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR A1050 " --> pdb=" O ILE A1045 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1074 Processing helix chain 'A' and resid 1092 through 1127 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 393 through 400 removed outlier: 3.641A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 459 through 478 removed outlier: 5.130A pdb=" N MET B 470 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP B 471 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN B 472 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL B 473 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 507 through 516 removed outlier: 3.687A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 587 removed outlier: 3.688A pdb=" N SER B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 620 removed outlier: 3.612A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B 620 " --> pdb=" O TRP B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 645 through 659 removed outlier: 3.613A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 668 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 686 No H-bonds generated for 'chain 'B' and resid 683 through 686' Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 707 through 714 removed outlier: 5.437A pdb=" N TYR B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 714 " --> pdb=" O SER B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 removed outlier: 3.704A pdb=" N ILE B 719 " --> pdb=" O GLU B 716 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 720 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 721 " --> pdb=" O ARG B 718 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 725 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 773 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 780 Processing helix chain 'B' and resid 785 through 806 Processing helix chain 'B' and resid 808 through 827 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 831 through 855 Processing helix chain 'B' and resid 863 through 892 Processing helix chain 'B' and resid 918 through 931 Processing helix chain 'B' and resid 936 through 940 removed outlier: 4.103A pdb=" N LEU B 939 " --> pdb=" O TRP B 936 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR B 940 " --> pdb=" O HIS B 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 936 through 940' Processing helix chain 'B' and resid 942 through 947 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 956 through 963 Processing helix chain 'B' and resid 998 through 1014 Processing helix chain 'B' and resid 1028 through 1059 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) removed outlier: 5.046A pdb=" N TRP B1047 " --> pdb=" O LEU B1042 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL B1048 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE B1049 " --> pdb=" O ILE B1044 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B1050 " --> pdb=" O ILE B1045 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1074 Processing helix chain 'B' and resid 1092 through 1127 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= A, first strand: chain 'A' and resid 388 through 390 Processing sheet with id= B, 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: 6.927A pdb=" N ILE A 733 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ALA A 627 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A 735 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY A 629 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS A 737 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 630 through 633 Processing sheet with id= D, 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= E, first strand: chain 'B' and resid 388 through 390 Processing sheet with id= F, 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: 6.927A pdb=" N ILE B 733 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA B 627 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS B 735 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY B 629 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS B 737 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 630 through 633 Processing sheet with id= H, 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) 524 hydrogen bonds defined for protein. 1512 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: 3.30 Time building geometry restraints manager: 4.67 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: 10337 3.28 - 3.82: 16591 3.82 - 4.36: 19758 4.36 - 4.90: 34552 Nonbonded interactions: 82557 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 82552 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.990 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 32.290 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.480 ------------------------------------------------------------------------------- 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= 0.795 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 : 1.241 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.9583 time to fit residues: 239.2597 Evaluate side-chains 140 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7146 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 459 HIS 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10624 Z= 0.145 Angle : 0.463 5.959 14488 Z= 0.248 Chirality : 0.039 0.152 1698 Planarity : 0.004 0.060 1798 Dihedral : 5.150 33.608 1562 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.88 % Allowed : 10.04 % Favored : 87.08 % 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: 0.28 (0.23), residues: 1346 helix: 1.39 (0.19), residues: 766 sheet: -1.30 (0.38), residues: 144 loop : -1.44 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 779 HIS 0.007 0.001 HIS B 828 PHE 0.014 0.001 PHE A 766 TYR 0.020 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 188 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.304 Fit side-chains outliers start: 29 outliers final: 7 residues processed: 177 average time/residue: 0.7947 time to fit residues: 157.7602 Evaluate side-chains 129 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.0951 time to fit residues: 2.0202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 0.0170 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN B 459 HIS B 828 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10624 Z= 0.197 Angle : 0.468 9.007 14488 Z= 0.249 Chirality : 0.039 0.148 1698 Planarity : 0.004 0.052 1798 Dihedral : 4.958 40.899 1562 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.18 % Allowed : 13.42 % Favored : 83.40 % 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: 0.79 (0.23), residues: 1346 helix: 1.74 (0.19), residues: 762 sheet: -0.56 (0.41), residues: 142 loop : -1.28 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1103 HIS 0.009 0.001 HIS B 828 PHE 0.021 0.001 PHE B 881 TYR 0.020 0.001 TYR B 827 ARG 0.004 0.000 ARG A 759 *********************** 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 169 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.189 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 155 average time/residue: 0.8266 time to fit residues: 142.9882 Evaluate side-chains 130 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.2684 time to fit residues: 3.8035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 HIS A 892 GLN A 965 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10624 Z= 0.326 Angle : 0.525 5.994 14488 Z= 0.280 Chirality : 0.042 0.147 1698 Planarity : 0.004 0.051 1798 Dihedral : 5.310 41.987 1562 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.78 % Allowed : 14.02 % 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: 0.82 (0.23), residues: 1346 helix: 1.81 (0.19), residues: 738 sheet: -0.41 (0.42), residues: 142 loop : -1.25 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.009 0.002 HIS B 536 PHE 0.020 0.002 PHE B 766 TYR 0.020 0.002 TYR B 827 ARG 0.004 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 158 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.194 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 143 average time/residue: 0.8896 time to fit residues: 141.3098 Evaluate side-chains 136 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.2393 time to fit residues: 3.9097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 0.0370 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10624 Z= 0.163 Angle : 0.448 6.302 14488 Z= 0.237 Chirality : 0.039 0.144 1698 Planarity : 0.003 0.044 1798 Dihedral : 4.692 35.611 1562 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 1.22 (0.23), residues: 1346 helix: 2.11 (0.19), residues: 740 sheet: -0.11 (0.43), residues: 142 loop : -1.08 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1103 HIS 0.005 0.001 HIS B 536 PHE 0.016 0.001 PHE B 881 TYR 0.017 0.001 TYR B 827 ARG 0.002 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 156 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 1.177 Fit side-chains outliers start: 37 outliers final: 20 residues processed: 143 average time/residue: 0.8951 time to fit residues: 141.7688 Evaluate side-chains 136 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.3442 time to fit residues: 4.9285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN B 658 ASN B 706 HIS B 934 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3721 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= 0.164 Angle : 0.440 6.409 14488 Z= 0.232 Chirality : 0.039 0.140 1698 Planarity : 0.003 0.046 1798 Dihedral : 4.543 35.192 1562 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.18 % Allowed : 15.81 % Favored : 81.01 % 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: 1.44 (0.23), residues: 1346 helix: 2.31 (0.19), residues: 732 sheet: 0.14 (0.44), residues: 142 loop : -1.00 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 806 HIS 0.004 0.001 HIS B 536 PHE 0.016 0.001 PHE B 766 TYR 0.017 0.001 TYR B 827 ARG 0.002 0.000 ARG A 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 154 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.207 Fit side-chains outliers start: 32 outliers final: 20 residues processed: 144 average time/residue: 0.9286 time to fit residues: 149.1616 Evaluate side-chains 136 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.7994 time to fit residues: 7.0638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 133 optimal weight: 0.4980 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN B 934 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3821 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= 0.141 Angle : 0.442 7.372 14488 Z= 0.230 Chirality : 0.039 0.148 1698 Planarity : 0.003 0.044 1798 Dihedral : 4.354 32.441 1562 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 16.10 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.23), residues: 1346 helix: 2.44 (0.19), residues: 736 sheet: 0.22 (0.44), residues: 142 loop : -0.85 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1103 HIS 0.004 0.001 HIS B 536 PHE 0.020 0.001 PHE B 881 TYR 0.026 0.001 TYR B1067 ARG 0.002 0.000 ARG A 464 *********************** 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 151 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.359 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 142 average time/residue: 0.8379 time to fit residues: 133.1465 Evaluate side-chains 136 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.3019 time to fit residues: 3.6112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3875 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= 0.225 Angle : 0.469 6.499 14488 Z= 0.246 Chirality : 0.040 0.242 1698 Planarity : 0.003 0.046 1798 Dihedral : 4.719 38.746 1562 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.88 % Allowed : 16.60 % Favored : 80.52 % 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: 1.56 (0.23), residues: 1346 helix: 2.38 (0.19), residues: 732 sheet: 0.19 (0.43), residues: 142 loop : -0.90 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 806 HIS 0.005 0.001 HIS B 536 PHE 0.018 0.001 PHE B 766 TYR 0.019 0.001 TYR A1067 ARG 0.002 0.000 ARG B 508 *********************** 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 146 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.090 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 139 average time/residue: 0.7997 time to fit residues: 124.5248 Evaluate side-chains 137 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 6 average time/residue: 0.5818 time to fit residues: 5.6624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10624 Z= 0.152 Angle : 0.452 8.226 14488 Z= 0.233 Chirality : 0.039 0.230 1698 Planarity : 0.003 0.044 1798 Dihedral : 4.317 31.997 1562 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.29 % Allowed : 17.20 % Favored : 80.52 % 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: 1.72 (0.23), residues: 1346 helix: 2.45 (0.19), residues: 744 sheet: 0.41 (0.43), residues: 142 loop : -0.86 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1103 HIS 0.004 0.001 HIS B 536 PHE 0.025 0.001 PHE B 881 TYR 0.028 0.001 TYR B1067 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 146 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.101 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 0.7829 time to fit residues: 123.3939 Evaluate side-chains 129 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1028 time to fit residues: 1.9943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7642 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10624 Z= 0.174 Angle : 0.468 9.420 14488 Z= 0.242 Chirality : 0.039 0.260 1698 Planarity : 0.003 0.045 1798 Dihedral : 4.418 34.278 1562 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.69 % Allowed : 17.89 % Favored : 80.42 % 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: 1.76 (0.23), residues: 1346 helix: 2.45 (0.19), residues: 744 sheet: 0.51 (0.44), residues: 142 loop : -0.83 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 806 HIS 0.005 0.001 HIS B 536 PHE 0.017 0.001 PHE B 766 TYR 0.026 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 130 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.396 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 128 average time/residue: 0.8512 time to fit residues: 122.7100 Evaluate side-chains 126 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.2577 time to fit residues: 1.9894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117981 restraints weight = 12573.255| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.01 r_work: 0.3253 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10624 Z= 0.144 Angle : 0.444 8.285 14488 Z= 0.230 Chirality : 0.039 0.259 1698 Planarity : 0.003 0.043 1798 Dihedral : 4.202 30.929 1562 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.69 % Allowed : 17.89 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1346 helix: 2.62 (0.19), residues: 732 sheet: 0.59 (0.45), residues: 142 loop : -0.74 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 779 HIS 0.004 0.001 HIS B 536 PHE 0.025 0.001 PHE B 881 TYR 0.036 0.001 TYR B1067 ARG 0.003 0.000 ARG A 759 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.50 seconds wall clock time: 60 minutes 8.14 seconds (3608.14 seconds total)