Starting phenix.real_space_refine on Sun Feb 18 08:43:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb4_31514/02_2024/7fb4_31514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb4_31514/02_2024/7fb4_31514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb4_31514/02_2024/7fb4_31514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb4_31514/02_2024/7fb4_31514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb4_31514/02_2024/7fb4_31514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb4_31514/02_2024/7fb4_31514.pdb" } resolution = 3.4 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= 0.076 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 97 5.16 5 C 13669 2.51 5 N 3560 2.21 5 O 4085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6635 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 41, 'TRANS': 809} Chain breaks: 7 Chain: "B" Number of atoms: 6632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6632 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 42, 'TRANS': 809} Chain breaks: 7 Chain: "C" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8144 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 53, 'TRANS': 989} Chain breaks: 6 Time building chain proxies: 11.41, per 1000 atoms: 0.53 Number of scatterers: 21411 At special positions: 0 Unit cell: (142.8, 133.28, 176.8, 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 97 16.00 O 4085 8.00 N 3560 7.00 C 13669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 8.03 Conformation dependent library (CDL) restraints added in 4.1 seconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5156 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 47 sheets defined 25.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.608A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.676A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.493A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 889 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.534A pdb=" N VAL A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.979A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.653A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.651A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.309A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 754 through 758 removed outlier: 3.855A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 758' Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.663A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.622A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.647A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.778A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.391A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.434A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.055A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.569A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.419A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.602A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 917 removed outlier: 4.175A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.451A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.086A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.974A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.845A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.098A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 197 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.578A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.413A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.146A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.924A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 4.967A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.692A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 212 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.692A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.723A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 310 through 319 removed outlier: 6.623A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG B 319 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER B 591 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.641A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.456A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.475A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1080 through 1082 Processing sheet with id=AC9, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD1, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.728A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.893A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.142A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.617A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.537A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 275 through 278 removed outlier: 3.731A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.271A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG C 319 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N SER C 591 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.832A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.926A pdb=" N GLU C 516 " --> pdb=" O THR C 393 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.510A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 553 through 554 removed outlier: 6.609A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.140A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.632A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 796 hydrogen bonds defined for protein. 2136 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: 8.60 Time building geometry restraints manager: 8.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6948 1.35 - 1.48: 5538 1.48 - 1.61: 9267 1.61 - 1.74: 0 1.74 - 1.87: 126 Bond restraints: 21879 Sorted by residual: bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.19e-02 7.06e+03 6.48e+00 bond pdb=" C VAL A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.83e-02 1.25e+03 5.44e+00 bond pdb=" C GLU A1111 " pdb=" N PRO A1112 " ideal model delta sigma weight residual 1.335 1.315 0.020 8.70e-03 1.32e+04 5.08e+00 bond pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 1.808 1.874 -0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.333 1.280 0.053 2.74e-02 1.33e+03 3.69e+00 ... (remaining 21874 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.65: 638 106.65 - 113.68: 12231 113.68 - 120.71: 8973 120.71 - 127.74: 7788 127.74 - 134.77: 135 Bond angle restraints: 29765 Sorted by residual: angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 128.39 -13.99 2.30e+00 1.89e-01 3.70e+01 angle pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" C ASN A 603 " ideal model delta sigma weight residual 114.39 106.16 8.23 1.45e+00 4.76e-01 3.22e+01 angle pdb=" C ARG B 328 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 121.80 134.77 -12.97 2.44e+00 1.68e-01 2.82e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.79 116.73 -7.94 1.53e+00 4.27e-01 2.69e+01 angle pdb=" C LYS A 790 " pdb=" N THR A 791 " pdb=" CA THR A 791 " ideal model delta sigma weight residual 120.68 113.29 7.39 1.52e+00 4.33e-01 2.36e+01 ... (remaining 29760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11811 17.87 - 35.74: 1036 35.74 - 53.61: 169 53.61 - 71.48: 34 71.48 - 89.35: 31 Dihedral angle restraints: 13081 sinusoidal: 5098 harmonic: 7983 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 3.35 -89.35 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.35 -80.65 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -11.97 -74.03 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 13078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2639 0.052 - 0.104: 675 0.104 - 0.156: 100 0.156 - 0.208: 6 0.208 - 0.260: 3 Chirality restraints: 3423 Sorted by residual: chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA CYS C 432 " pdb=" N CYS C 432 " pdb=" C CYS C 432 " pdb=" CB CYS C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3420 not shown) Planarity restraints: 3859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 329 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 330 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 588 " 0.040 5.00e-02 4.00e+02 6.16e-02 6.06e+00 pdb=" N PRO B 589 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1078 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO B1079 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B1079 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1079 " 0.028 5.00e-02 4.00e+02 ... (remaining 3856 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1110 2.71 - 3.26: 22563 3.26 - 3.81: 34061 3.81 - 4.35: 41208 4.35 - 4.90: 70211 Nonbonded interactions: 169153 Sorted by model distance: nonbonded pdb=" OD1 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.164 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 191 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE2 GLU A 619 " model vdw 2.189 2.440 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.209 2.440 ... (remaining 169148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 143 or resid 154 through 245 or resid 259 throu \ gh 1146)) selection = (chain 'B' and (resid 24 through 245 or resid 259 through 528 or resid 530 throu \ gh 620 or resid 641 through 828 or resid 850 through 1146)) } 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=0.00 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: 0.810 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: 0.020 Extract box with map and model: 4.900 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 58.890 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.005 0.066 21879 Z= 0.332 Angle : 0.713 13.992 29765 Z= 0.412 Chirality : 0.046 0.260 3423 Planarity : 0.004 0.064 3859 Dihedral : 14.046 88.643 7835 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.08 % Allowed : 5.83 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.07 (0.14), residues: 2700 helix: -0.18 (0.20), residues: 587 sheet: -3.26 (0.17), residues: 581 loop : -3.68 (0.13), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 PHE 0.022 0.002 PHE A 906 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6818 (m-10) cc_final: 0.6569 (m-10) REVERT: A 740 MET cc_start: 0.8863 (tpt) cc_final: 0.8620 (tpt) REVERT: A 988 GLU cc_start: 0.8837 (tp30) cc_final: 0.8538 (tp30) REVERT: A 990 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 1138 TYR cc_start: 0.8015 (t80) cc_final: 0.7613 (t80) REVERT: B 54 LEU cc_start: 0.8882 (mm) cc_final: 0.8577 (mm) REVERT: B 88 ASP cc_start: 0.7835 (p0) cc_final: 0.6995 (p0) REVERT: B 177 MET cc_start: 0.0044 (mtp) cc_final: -0.0474 (mtm) REVERT: B 731 MET cc_start: 0.9336 (ptt) cc_final: 0.9078 (ptm) REVERT: B 787 GLN cc_start: 0.8415 (mm110) cc_final: 0.8207 (mp10) REVERT: B 997 ILE cc_start: 0.9305 (mt) cc_final: 0.9041 (mt) REVERT: C 200 TYR cc_start: 0.9091 (m-80) cc_final: 0.8780 (m-10) REVERT: C 270 LEU cc_start: 0.9290 (mt) cc_final: 0.8998 (mp) REVERT: C 421 TYR cc_start: 0.8730 (m-80) cc_final: 0.8133 (m-10) REVERT: C 762 GLN cc_start: 0.8358 (mt0) cc_final: 0.8143 (mt0) REVERT: C 787 GLN cc_start: 0.8422 (mp10) cc_final: 0.7899 (mt0) REVERT: C 995 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8539 (ttm-80) REVERT: C 1002 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8671 (mm-40) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.3472 time to fit residues: 109.7288 Evaluate side-chains 130 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 159 optimal weight: 0.4980 chunk 248 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 99 ASN A 134 GLN A 188 ASN A 282 ASN A 580 GLN A 675 GLN A 690 GLN A 751 ASN A 755 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 901 GLN A 954 GLN A 955 ASN A 969 ASN A1054 GLN A1088 HIS B 115 GLN B 211 ASN B 218 GLN B 317 ASN B 762 GLN B 919 ASN B 925 ASN B 954 GLN B 965 GLN B 992 GLN B1023 ASN B1071 GLN B1074 ASN B1106 GLN C 69 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 207 HIS C 218 GLN C 271 GLN C 343 ASN C 448 ASN C 751 ASN C 920 GLN C 925 ASN C 954 GLN C 965 GLN C 969 ASN C1023 ASN C1058 HIS C1064 HIS C1074 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21879 Z= 0.186 Angle : 0.581 12.366 29765 Z= 0.299 Chirality : 0.044 0.235 3423 Planarity : 0.004 0.063 3859 Dihedral : 4.916 40.105 2912 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.12 % Allowed : 10.45 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.16), residues: 2700 helix: 1.58 (0.22), residues: 594 sheet: -2.62 (0.19), residues: 595 loop : -3.17 (0.14), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.005 0.001 HIS C1048 PHE 0.029 0.001 PHE C 855 TYR 0.016 0.001 TYR B 660 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.8122 (m-10) cc_final: 0.7919 (m-10) REVERT: A 200 TYR cc_start: 0.8927 (m-10) cc_final: 0.8518 (m-10) REVERT: A 329 PHE cc_start: 0.6915 (m-10) cc_final: 0.6599 (m-10) REVERT: A 661 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 988 GLU cc_start: 0.8854 (tp30) cc_final: 0.8541 (tp30) REVERT: A 990 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 1138 TYR cc_start: 0.8005 (t80) cc_final: 0.7621 (t80) REVERT: B 54 LEU cc_start: 0.8939 (mm) cc_final: 0.8660 (mm) REVERT: B 88 ASP cc_start: 0.7872 (p0) cc_final: 0.7106 (p0) REVERT: B 102 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8125 (ttm110) REVERT: B 177 MET cc_start: -0.0031 (mtp) cc_final: -0.0623 (mtm) REVERT: B 198 ASP cc_start: 0.9230 (m-30) cc_final: 0.8973 (m-30) REVERT: B 237 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7843 (ttm110) REVERT: B 299 THR cc_start: 0.8991 (m) cc_final: 0.8717 (p) REVERT: B 699 LEU cc_start: 0.8983 (mt) cc_final: 0.8646 (mt) REVERT: B 731 MET cc_start: 0.9367 (ptt) cc_final: 0.9106 (ptm) REVERT: B 756 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: B 759 PHE cc_start: 0.8623 (m-80) cc_final: 0.8406 (m-80) REVERT: B 776 LYS cc_start: 0.8873 (tppt) cc_final: 0.8451 (tppt) REVERT: B 780 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 1017 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7880 (tm-30) REVERT: C 200 TYR cc_start: 0.9063 (m-80) cc_final: 0.8800 (m-10) REVERT: C 365 TYR cc_start: 0.7755 (p90) cc_final: 0.7132 (p90) REVERT: C 421 TYR cc_start: 0.8938 (m-80) cc_final: 0.8168 (m-10) REVERT: C 762 GLN cc_start: 0.8427 (mt0) cc_final: 0.8186 (mt0) REVERT: C 787 GLN cc_start: 0.8567 (mp10) cc_final: 0.8215 (mt0) REVERT: C 995 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8423 (ttm-80) REVERT: C 1002 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8675 (mm-40) outliers start: 27 outliers final: 11 residues processed: 175 average time/residue: 0.3050 time to fit residues: 86.9212 Evaluate side-chains 139 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 169 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 269 optimal weight: 0.5980 chunk 221 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A1064 HIS B 955 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 544 ASN C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 21879 Z= 0.231 Angle : 0.575 12.172 29765 Z= 0.294 Chirality : 0.043 0.202 3423 Planarity : 0.004 0.061 3859 Dihedral : 4.776 39.066 2912 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.00 % Allowed : 12.62 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.16), residues: 2700 helix: 1.96 (0.22), residues: 594 sheet: -2.33 (0.19), residues: 589 loop : -2.91 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS C1048 PHE 0.020 0.001 PHE B 329 TYR 0.012 0.001 TYR C 505 ARG 0.002 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 143 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.8159 (m-10) cc_final: 0.7820 (m-10) REVERT: A 200 TYR cc_start: 0.8959 (m-10) cc_final: 0.8585 (m-10) REVERT: A 223 LEU cc_start: 0.7812 (mt) cc_final: 0.7548 (mt) REVERT: A 294 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: A 329 PHE cc_start: 0.6941 (m-10) cc_final: 0.6605 (m-10) REVERT: A 773 GLU cc_start: 0.8435 (tp30) cc_final: 0.8175 (tt0) REVERT: A 988 GLU cc_start: 0.8857 (tp30) cc_final: 0.8560 (tp30) REVERT: A 990 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8150 (mm-30) REVERT: A 1138 TYR cc_start: 0.8028 (t80) cc_final: 0.7599 (t80) REVERT: A 1141 LEU cc_start: 0.8644 (tp) cc_final: 0.8358 (tt) REVERT: B 54 LEU cc_start: 0.8956 (mm) cc_final: 0.8656 (mm) REVERT: B 88 ASP cc_start: 0.7856 (p0) cc_final: 0.6995 (p0) REVERT: B 102 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8111 (ttm110) REVERT: B 177 MET cc_start: 0.0041 (mtp) cc_final: -0.0464 (mtm) REVERT: B 237 ARG cc_start: 0.8604 (mtm110) cc_final: 0.7973 (ttp-170) REVERT: B 299 THR cc_start: 0.9026 (m) cc_final: 0.8742 (p) REVERT: B 699 LEU cc_start: 0.8986 (mt) cc_final: 0.8701 (mt) REVERT: B 731 MET cc_start: 0.9384 (ptt) cc_final: 0.9118 (ptm) REVERT: B 756 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: B 776 LYS cc_start: 0.9069 (tppt) cc_final: 0.8694 (tppt) REVERT: B 780 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 1017 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7936 (tm-30) REVERT: C 55 PHE cc_start: 0.9128 (m-80) cc_final: 0.8924 (m-80) REVERT: C 200 TYR cc_start: 0.9077 (m-80) cc_final: 0.8834 (m-80) REVERT: C 421 TYR cc_start: 0.8924 (m-80) cc_final: 0.8132 (m-10) REVERT: C 787 GLN cc_start: 0.8576 (mp10) cc_final: 0.8179 (mt0) REVERT: C 1002 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8673 (mm-40) outliers start: 48 outliers final: 28 residues processed: 182 average time/residue: 0.2962 time to fit residues: 89.0142 Evaluate side-chains 157 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 130 optimal weight: 0.0050 chunk 237 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 544 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN C 99 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 21879 Z= 0.158 Angle : 0.539 14.312 29765 Z= 0.276 Chirality : 0.043 0.209 3423 Planarity : 0.004 0.064 3859 Dihedral : 4.544 38.180 2912 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.83 % Allowed : 13.66 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.16), residues: 2700 helix: 2.13 (0.22), residues: 606 sheet: -2.10 (0.20), residues: 599 loop : -2.74 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS C1048 PHE 0.027 0.001 PHE B 92 TYR 0.020 0.001 TYR C 365 ARG 0.007 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8921 (m-10) cc_final: 0.8631 (m-10) REVERT: A 294 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: A 329 PHE cc_start: 0.6888 (m-10) cc_final: 0.6533 (m-10) REVERT: A 661 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 774 GLN cc_start: 0.8510 (mm-40) cc_final: 0.7599 (mm-40) REVERT: A 988 GLU cc_start: 0.8849 (tp30) cc_final: 0.8560 (tp30) REVERT: A 1138 TYR cc_start: 0.8001 (t80) cc_final: 0.7550 (t80) REVERT: A 1141 LEU cc_start: 0.8625 (tp) cc_final: 0.8374 (tt) REVERT: B 54 LEU cc_start: 0.8877 (mm) cc_final: 0.8548 (mm) REVERT: B 88 ASP cc_start: 0.7837 (p0) cc_final: 0.6930 (p0) REVERT: B 102 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8121 (tpp80) REVERT: B 177 MET cc_start: -0.0070 (mtp) cc_final: -0.0601 (mtm) REVERT: B 237 ARG cc_start: 0.8612 (mtm110) cc_final: 0.7930 (ttp-110) REVERT: B 299 THR cc_start: 0.9010 (m) cc_final: 0.8745 (p) REVERT: B 731 MET cc_start: 0.9419 (ptt) cc_final: 0.9158 (ptm) REVERT: B 756 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: B 776 LYS cc_start: 0.9098 (tppt) cc_final: 0.8612 (tppt) REVERT: B 780 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7318 (mm-30) REVERT: B 900 MET cc_start: 0.8462 (mtp) cc_final: 0.8018 (mtt) REVERT: B 1017 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7925 (tm-30) REVERT: C 200 TYR cc_start: 0.9018 (m-80) cc_final: 0.8804 (m-80) REVERT: C 275 PHE cc_start: 0.8900 (m-10) cc_final: 0.8556 (m-10) REVERT: C 421 TYR cc_start: 0.8943 (m-80) cc_final: 0.8159 (m-10) REVERT: C 787 GLN cc_start: 0.8582 (mp10) cc_final: 0.8196 (mt0) REVERT: C 1002 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8601 (mm-40) outliers start: 44 outliers final: 29 residues processed: 180 average time/residue: 0.2808 time to fit residues: 85.0656 Evaluate side-chains 153 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 0 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21879 Z= 0.285 Angle : 0.579 13.695 29765 Z= 0.297 Chirality : 0.043 0.208 3423 Planarity : 0.004 0.062 3859 Dihedral : 4.639 37.263 2912 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.21 % Allowed : 14.83 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.16), residues: 2700 helix: 2.13 (0.22), residues: 606 sheet: -1.98 (0.21), residues: 564 loop : -2.67 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS C1083 PHE 0.019 0.001 PHE B 92 TYR 0.014 0.001 TYR A 91 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 127 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 CYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5369 (t) REVERT: A 194 PHE cc_start: 0.8300 (m-10) cc_final: 0.7936 (m-10) REVERT: A 200 TYR cc_start: 0.8996 (m-10) cc_final: 0.8669 (m-10) REVERT: A 223 LEU cc_start: 0.7943 (mt) cc_final: 0.7686 (mt) REVERT: A 329 PHE cc_start: 0.7010 (m-10) cc_final: 0.6617 (m-10) REVERT: A 988 GLU cc_start: 0.8909 (tp30) cc_final: 0.8647 (tp30) REVERT: A 1017 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 1138 TYR cc_start: 0.8031 (t80) cc_final: 0.7555 (t80) REVERT: A 1141 LEU cc_start: 0.8644 (tp) cc_final: 0.8390 (tt) REVERT: B 54 LEU cc_start: 0.8971 (mm) cc_final: 0.8652 (mm) REVERT: B 88 ASP cc_start: 0.7866 (p0) cc_final: 0.6915 (p0) REVERT: B 102 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8137 (tpp80) REVERT: B 177 MET cc_start: 0.0709 (mtp) cc_final: 0.0233 (mtm) REVERT: B 237 ARG cc_start: 0.8547 (mtm110) cc_final: 0.7951 (ttp-110) REVERT: B 299 THR cc_start: 0.9025 (m) cc_final: 0.8740 (p) REVERT: B 699 LEU cc_start: 0.9011 (mt) cc_final: 0.8693 (mt) REVERT: B 731 MET cc_start: 0.9385 (ptt) cc_final: 0.9137 (ptm) REVERT: B 756 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: B 776 LYS cc_start: 0.9136 (tppt) cc_final: 0.8616 (tppt) REVERT: B 780 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7423 (mm-30) REVERT: C 200 TYR cc_start: 0.9029 (m-80) cc_final: 0.8808 (m-80) REVERT: C 421 TYR cc_start: 0.8955 (m-80) cc_final: 0.8201 (m-10) REVERT: C 787 GLN cc_start: 0.8620 (mp10) cc_final: 0.8226 (mt0) REVERT: C 1002 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8676 (mm-40) outliers start: 53 outliers final: 40 residues processed: 172 average time/residue: 0.2787 time to fit residues: 80.7062 Evaluate side-chains 163 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS C 99 ASN C 762 GLN C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21879 Z= 0.166 Angle : 0.533 13.164 29765 Z= 0.272 Chirality : 0.042 0.196 3423 Planarity : 0.004 0.064 3859 Dihedral : 4.452 36.734 2912 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.25 % Allowed : 15.24 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2700 helix: 2.25 (0.22), residues: 611 sheet: -1.78 (0.21), residues: 561 loop : -2.55 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.004 0.000 HIS C1048 PHE 0.020 0.001 PHE B 92 TYR 0.016 0.001 TYR C 365 ARG 0.003 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 CYS cc_start: 0.5858 (OUTLIER) cc_final: 0.5344 (t) REVERT: A 194 PHE cc_start: 0.8100 (m-10) cc_final: 0.7584 (m-10) REVERT: A 200 TYR cc_start: 0.8944 (m-10) cc_final: 0.8629 (m-10) REVERT: A 294 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: A 329 PHE cc_start: 0.6987 (m-10) cc_final: 0.6586 (m-10) REVERT: A 661 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7367 (tm-30) REVERT: A 988 GLU cc_start: 0.8888 (tp30) cc_final: 0.8652 (tp30) REVERT: A 1017 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 1138 TYR cc_start: 0.8032 (t80) cc_final: 0.7558 (t80) REVERT: A 1141 LEU cc_start: 0.8731 (tp) cc_final: 0.8497 (tt) REVERT: B 54 LEU cc_start: 0.8868 (mm) cc_final: 0.8546 (mm) REVERT: B 88 ASP cc_start: 0.7800 (p0) cc_final: 0.6861 (p0) REVERT: B 102 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8120 (tpp80) REVERT: B 177 MET cc_start: 0.0579 (mtp) cc_final: 0.0091 (mtm) REVERT: B 237 ARG cc_start: 0.8555 (mtm110) cc_final: 0.7979 (ttp-110) REVERT: B 299 THR cc_start: 0.8964 (m) cc_final: 0.8700 (p) REVERT: B 699 LEU cc_start: 0.8925 (mt) cc_final: 0.8615 (mt) REVERT: B 731 MET cc_start: 0.9419 (ptt) cc_final: 0.9166 (ptm) REVERT: B 756 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: B 776 LYS cc_start: 0.9097 (tppt) cc_final: 0.8600 (tppt) REVERT: B 780 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7405 (mm-30) REVERT: B 900 MET cc_start: 0.8434 (mtp) cc_final: 0.7990 (mtt) REVERT: B 902 MET cc_start: 0.8893 (tpt) cc_final: 0.8370 (tpt) REVERT: B 957 GLN cc_start: 0.8679 (tt0) cc_final: 0.8398 (tt0) REVERT: C 200 TYR cc_start: 0.9030 (m-80) cc_final: 0.8829 (m-80) REVERT: C 275 PHE cc_start: 0.8891 (m-10) cc_final: 0.8666 (m-10) REVERT: C 421 TYR cc_start: 0.8949 (m-80) cc_final: 0.8200 (m-10) REVERT: C 787 GLN cc_start: 0.8610 (mp10) cc_final: 0.8265 (mt0) REVERT: C 1002 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8596 (mm-40) outliers start: 54 outliers final: 40 residues processed: 183 average time/residue: 0.3050 time to fit residues: 93.0466 Evaluate side-chains 168 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 762 GLN C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21879 Z= 0.251 Angle : 0.559 12.978 29765 Z= 0.287 Chirality : 0.043 0.257 3423 Planarity : 0.004 0.064 3859 Dihedral : 4.513 35.627 2912 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.50 % Allowed : 15.66 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.74 (0.17), residues: 2700 helix: 2.23 (0.22), residues: 611 sheet: -1.76 (0.21), residues: 582 loop : -2.49 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.004 0.001 HIS B1064 PHE 0.019 0.001 PHE B 329 TYR 0.013 0.001 TYR A 91 ARG 0.003 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 128 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 CYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5416 (t) REVERT: A 194 PHE cc_start: 0.8214 (m-10) cc_final: 0.7842 (m-10) REVERT: A 200 TYR cc_start: 0.8957 (m-10) cc_final: 0.8740 (m-10) REVERT: A 329 PHE cc_start: 0.7072 (m-10) cc_final: 0.6618 (m-10) REVERT: A 661 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 988 GLU cc_start: 0.8924 (tp30) cc_final: 0.8648 (tp30) REVERT: A 1017 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8098 (tm-30) REVERT: A 1138 TYR cc_start: 0.8041 (t80) cc_final: 0.7568 (t80) REVERT: A 1141 LEU cc_start: 0.8745 (tp) cc_final: 0.8506 (tt) REVERT: B 54 LEU cc_start: 0.8896 (mm) cc_final: 0.8573 (mm) REVERT: B 88 ASP cc_start: 0.7828 (p0) cc_final: 0.6888 (p0) REVERT: B 102 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8126 (tpp80) REVERT: B 177 MET cc_start: 0.0617 (mtp) cc_final: 0.0144 (mtm) REVERT: B 237 ARG cc_start: 0.8558 (mtm110) cc_final: 0.7967 (ttp-110) REVERT: B 299 THR cc_start: 0.8972 (m) cc_final: 0.8696 (p) REVERT: B 699 LEU cc_start: 0.8981 (mt) cc_final: 0.8711 (mt) REVERT: B 731 MET cc_start: 0.9389 (ptt) cc_final: 0.9138 (ptm) REVERT: B 756 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: B 776 LYS cc_start: 0.9133 (tppt) cc_final: 0.8625 (tppt) REVERT: B 780 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7457 (mm-30) REVERT: C 200 TYR cc_start: 0.9031 (m-80) cc_final: 0.8632 (m-80) REVERT: C 421 TYR cc_start: 0.8965 (m-80) cc_final: 0.8224 (m-10) REVERT: C 762 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8670 (pt0) REVERT: C 787 GLN cc_start: 0.8645 (mp10) cc_final: 0.8261 (mt0) REVERT: C 1002 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8613 (mm-40) outliers start: 60 outliers final: 43 residues processed: 178 average time/residue: 0.2758 time to fit residues: 83.4272 Evaluate side-chains 168 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 79 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 901 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21879 Z= 0.168 Angle : 0.527 12.678 29765 Z= 0.270 Chirality : 0.042 0.196 3423 Planarity : 0.004 0.064 3859 Dihedral : 4.363 35.108 2912 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.21 % Allowed : 16.49 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.62 (0.17), residues: 2700 helix: 2.30 (0.22), residues: 608 sheet: -1.65 (0.21), residues: 578 loop : -2.40 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.005 0.001 HIS B1064 PHE 0.018 0.001 PHE B 329 TYR 0.014 0.001 TYR C 365 ARG 0.003 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 135 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: A 166 CYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5448 (t) REVERT: A 194 PHE cc_start: 0.7912 (m-10) cc_final: 0.7613 (m-10) REVERT: A 200 TYR cc_start: 0.8897 (m-10) cc_final: 0.8683 (m-10) REVERT: A 329 PHE cc_start: 0.7068 (m-10) cc_final: 0.6821 (m-10) REVERT: A 661 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 774 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7560 (mm-40) REVERT: A 988 GLU cc_start: 0.8908 (tp30) cc_final: 0.8496 (tp30) REVERT: A 1017 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 1138 TYR cc_start: 0.8052 (t80) cc_final: 0.7550 (t80) REVERT: A 1141 LEU cc_start: 0.8716 (tp) cc_final: 0.8490 (tt) REVERT: B 54 LEU cc_start: 0.8862 (mm) cc_final: 0.8544 (mm) REVERT: B 88 ASP cc_start: 0.7752 (p0) cc_final: 0.6813 (p0) REVERT: B 177 MET cc_start: 0.0533 (mtp) cc_final: 0.0060 (mtm) REVERT: B 237 ARG cc_start: 0.8580 (mtm110) cc_final: 0.8023 (ttp-110) REVERT: B 299 THR cc_start: 0.8954 (m) cc_final: 0.8692 (p) REVERT: B 699 LEU cc_start: 0.8922 (mt) cc_final: 0.8624 (mt) REVERT: B 731 MET cc_start: 0.9421 (ptt) cc_final: 0.9180 (ptm) REVERT: B 756 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: B 776 LYS cc_start: 0.9098 (tppt) cc_final: 0.8598 (tppt) REVERT: B 780 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7473 (mm-30) REVERT: B 900 MET cc_start: 0.8438 (mtp) cc_final: 0.8003 (mtt) REVERT: B 902 MET cc_start: 0.8882 (tpt) cc_final: 0.8359 (tpt) REVERT: B 957 GLN cc_start: 0.8686 (tt0) cc_final: 0.8403 (tt0) REVERT: C 200 TYR cc_start: 0.9018 (m-80) cc_final: 0.8659 (m-80) REVERT: C 275 PHE cc_start: 0.8917 (m-10) cc_final: 0.8648 (m-10) REVERT: C 421 TYR cc_start: 0.8966 (m-80) cc_final: 0.8228 (m-10) REVERT: C 762 GLN cc_start: 0.8839 (pt0) cc_final: 0.8576 (pt0) REVERT: C 787 GLN cc_start: 0.8630 (mp10) cc_final: 0.8260 (mt0) REVERT: C 1002 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8582 (mm-40) outliers start: 53 outliers final: 43 residues processed: 178 average time/residue: 0.3232 time to fit residues: 97.6870 Evaluate side-chains 170 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 193 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21879 Z= 0.180 Angle : 0.526 12.506 29765 Z= 0.270 Chirality : 0.042 0.195 3423 Planarity : 0.004 0.066 3859 Dihedral : 4.326 34.233 2912 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.25 % Allowed : 16.74 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.55 (0.17), residues: 2700 helix: 2.32 (0.22), residues: 609 sheet: -1.53 (0.21), residues: 586 loop : -2.38 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.004 0.001 HIS B1064 PHE 0.025 0.001 PHE A 201 TYR 0.010 0.001 TYR C1067 ARG 0.008 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 132 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: A 166 CYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5455 (t) REVERT: A 194 PHE cc_start: 0.7949 (m-10) cc_final: 0.7671 (m-10) REVERT: A 200 TYR cc_start: 0.8884 (m-10) cc_final: 0.8646 (m-10) REVERT: A 329 PHE cc_start: 0.7021 (m-10) cc_final: 0.6776 (m-10) REVERT: A 661 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 774 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7564 (mm-40) REVERT: A 950 ASP cc_start: 0.8712 (m-30) cc_final: 0.8463 (m-30) REVERT: A 988 GLU cc_start: 0.8897 (tp30) cc_final: 0.8527 (tp30) REVERT: A 1017 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 1138 TYR cc_start: 0.8095 (t80) cc_final: 0.7583 (t80) REVERT: A 1141 LEU cc_start: 0.8710 (tp) cc_final: 0.8491 (tt) REVERT: B 54 LEU cc_start: 0.8870 (mm) cc_final: 0.8555 (mm) REVERT: B 88 ASP cc_start: 0.7750 (p0) cc_final: 0.6817 (p0) REVERT: B 177 MET cc_start: 0.0506 (mtp) cc_final: -0.0002 (mtm) REVERT: B 237 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8103 (ttp-110) REVERT: B 299 THR cc_start: 0.8950 (m) cc_final: 0.8689 (p) REVERT: B 699 LEU cc_start: 0.8946 (mt) cc_final: 0.8673 (mt) REVERT: B 731 MET cc_start: 0.9422 (ptt) cc_final: 0.9173 (ptm) REVERT: B 756 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: B 776 LYS cc_start: 0.9100 (tppt) cc_final: 0.8607 (tppt) REVERT: B 780 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7540 (mm-30) REVERT: B 902 MET cc_start: 0.8896 (tpt) cc_final: 0.8358 (tpt) REVERT: B 957 GLN cc_start: 0.8682 (tt0) cc_final: 0.8394 (tt0) REVERT: C 200 TYR cc_start: 0.9021 (m-80) cc_final: 0.8703 (m-80) REVERT: C 421 TYR cc_start: 0.8971 (m-80) cc_final: 0.8241 (m-10) REVERT: C 762 GLN cc_start: 0.8952 (pt0) cc_final: 0.8674 (pt0) REVERT: C 787 GLN cc_start: 0.8633 (mp10) cc_final: 0.8285 (mt0) REVERT: C 1002 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8552 (mm-40) outliers start: 54 outliers final: 44 residues processed: 177 average time/residue: 0.2740 time to fit residues: 82.1956 Evaluate side-chains 174 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 127 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 272 optimal weight: 3.9990 chunk 251 optimal weight: 0.6980 chunk 217 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21879 Z= 0.198 Angle : 0.539 12.564 29765 Z= 0.276 Chirality : 0.043 0.195 3423 Planarity : 0.004 0.066 3859 Dihedral : 4.313 33.476 2912 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.29 % Allowed : 16.83 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.51 (0.17), residues: 2700 helix: 2.31 (0.22), residues: 611 sheet: -1.44 (0.22), residues: 581 loop : -2.37 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.004 0.001 HIS B1064 PHE 0.019 0.001 PHE B 782 TYR 0.014 0.001 TYR C 365 ARG 0.006 0.000 ARG C 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 129 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: A 166 CYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5474 (t) REVERT: A 200 TYR cc_start: 0.8883 (m-10) cc_final: 0.8626 (m-10) REVERT: A 329 PHE cc_start: 0.7066 (m-10) cc_final: 0.6821 (m-10) REVERT: A 661 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 950 ASP cc_start: 0.8710 (m-30) cc_final: 0.8467 (m-30) REVERT: A 988 GLU cc_start: 0.8884 (tp30) cc_final: 0.8515 (tp30) REVERT: A 1017 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 1138 TYR cc_start: 0.8099 (t80) cc_final: 0.7588 (t80) REVERT: A 1141 LEU cc_start: 0.8704 (tp) cc_final: 0.8487 (tt) REVERT: B 54 LEU cc_start: 0.8873 (mm) cc_final: 0.8552 (mm) REVERT: B 88 ASP cc_start: 0.7736 (p0) cc_final: 0.6794 (p0) REVERT: B 177 MET cc_start: 0.0504 (mtp) cc_final: -0.0002 (mtm) REVERT: B 237 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8070 (ttp-110) REVERT: B 299 THR cc_start: 0.8951 (m) cc_final: 0.8685 (p) REVERT: B 699 LEU cc_start: 0.8948 (mt) cc_final: 0.8673 (mt) REVERT: B 731 MET cc_start: 0.9420 (ptt) cc_final: 0.9175 (ptm) REVERT: B 756 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: B 776 LYS cc_start: 0.9096 (tppt) cc_final: 0.8593 (tppt) REVERT: B 780 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7431 (mm-30) REVERT: B 957 GLN cc_start: 0.8683 (tt0) cc_final: 0.8397 (tt0) REVERT: C 200 TYR cc_start: 0.9023 (m-80) cc_final: 0.8704 (m-80) REVERT: C 275 PHE cc_start: 0.8960 (m-10) cc_final: 0.8669 (m-80) REVERT: C 421 TYR cc_start: 0.8979 (m-80) cc_final: 0.8251 (m-10) REVERT: C 697 MET cc_start: 0.8039 (ptm) cc_final: 0.7782 (ptm) REVERT: C 762 GLN cc_start: 0.8952 (pt0) cc_final: 0.8690 (pt0) REVERT: C 787 GLN cc_start: 0.8635 (mp10) cc_final: 0.8292 (mt0) REVERT: C 1002 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8567 (mm-40) outliers start: 55 outliers final: 45 residues processed: 173 average time/residue: 0.2838 time to fit residues: 83.0772 Evaluate side-chains 176 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 128 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** 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 = 0.3845 r_free = 0.3845 target = 0.121279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080768 restraints weight = 52791.147| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.39 r_work: 0.2925 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21879 Z= 0.193 Angle : 0.542 12.480 29765 Z= 0.275 Chirality : 0.042 0.194 3423 Planarity : 0.004 0.064 3859 Dihedral : 4.295 32.792 2912 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.21 % Allowed : 16.99 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.49 (0.17), residues: 2700 helix: 2.31 (0.22), residues: 611 sheet: -1.40 (0.22), residues: 580 loop : -2.36 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS B1064 PHE 0.041 0.001 PHE A 201 TYR 0.010 0.001 TYR C1067 ARG 0.009 0.000 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.96 seconds wall clock time: 73 minutes 5.92 seconds (4385.92 seconds total)