Starting phenix.real_space_refine on Mon Mar 18 16:40:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9e_24257/03_2024/7n9e_24257.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9e_24257/03_2024/7n9e_24257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9e_24257/03_2024/7n9e_24257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9e_24257/03_2024/7n9e_24257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9e_24257/03_2024/7n9e_24257.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9e_24257/03_2024/7n9e_24257.pdb" } resolution = 3.52 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= 0.004 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 96 5.16 5 C 13714 2.51 5 N 3615 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21460 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 858 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 7548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7548 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6197 Classifications: {'peptide': 809} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 44, 'TRANS': 764} Chain breaks: 7 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 6857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 6857 Classifications: {'peptide': 943} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 51, 'TRANS': 891} Chain breaks: 7 Unresolved non-hydrogen bonds: 511 Unresolved non-hydrogen angles: 657 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 293 Time building chain proxies: 10.19, per 1000 atoms: 0.47 Number of scatterers: 21460 At special positions: 0 Unit cell: (133.56, 129.32, 177.02, 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 96 16.00 O 4035 8.00 N 3615 7.00 C 13714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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=2.01 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=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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: 7.27 Conformation dependent library (CDL) restraints added in 4.1 seconds 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5370 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 44 sheets defined 26.9% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.509A pdb=" N LYS D 65 " --> pdb=" O SER D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 5.388A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.915A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 635 through 638 removed outlier: 3.854A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 638' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.746A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.716A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR A 827 " --> pdb=" O PHE A 823 " (cutoff:3.500A) 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 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.259A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.539A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.179A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.876A 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.265A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.600A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.901A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.938A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.567A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.514A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.686A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.013A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.547A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 957 Processing helix chain 'B' and resid 959 through 965 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.770A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1148 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.729A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.708A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.762A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.961A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 4.051A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.610A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.596A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.665A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.753A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.563A 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 989 through 1033 Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.785A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.566A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D 35 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 68 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.817A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.158A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.264A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.801A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.554A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.740A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.104A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.021A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.217A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.838A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.965A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.330A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.648A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.386A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.546A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.676A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.524A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 224 through 227 removed outlier: 6.981A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.984A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.116A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.376A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 659 through 660 removed outlier: 3.887A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.748A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.645A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 910 hydrogen bonds defined for protein. 2499 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: 9.29 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6138 1.33 - 1.45: 3427 1.45 - 1.58: 12245 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 21932 Sorted by residual: bond pdb=" C CYS C 361 " pdb=" O CYS C 361 " ideal model delta sigma weight residual 1.235 1.269 -0.034 9.00e-03 1.23e+04 1.43e+01 bond pdb=" CA SER C 708 " pdb=" CB SER C 708 " ideal model delta sigma weight residual 1.533 1.475 0.057 1.65e-02 3.67e+03 1.21e+01 bond pdb=" C LEU A 212 " pdb=" O LEU A 212 " ideal model delta sigma weight residual 1.234 1.276 -0.042 1.22e-02 6.72e+03 1.19e+01 bond pdb=" CA ALA D 61 " pdb=" CB ALA D 61 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.61e-02 3.86e+03 1.11e+01 bond pdb=" C CYS C 590 " pdb=" O CYS C 590 " ideal model delta sigma weight residual 1.234 1.274 -0.040 1.20e-02 6.94e+03 1.10e+01 ... (remaining 21927 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.23: 574 105.23 - 112.52: 11119 112.52 - 119.82: 9060 119.82 - 127.11: 9064 127.11 - 134.41: 118 Bond angle restraints: 29935 Sorted by residual: angle pdb=" N ALA D 75 " pdb=" CA ALA D 75 " pdb=" C ALA D 75 " ideal model delta sigma weight residual 111.28 119.67 -8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" C CYS C 361 " pdb=" CA CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sigma weight residual 114.10 99.72 14.38 2.11e+00 2.25e-01 4.65e+01 angle pdb=" N ASP C 88 " pdb=" CA ASP C 88 " pdb=" C ASP C 88 " ideal model delta sigma weight residual 114.62 107.21 7.41 1.14e+00 7.69e-01 4.23e+01 angle pdb=" N GLY D 26 " pdb=" CA GLY D 26 " pdb=" C GLY D 26 " ideal model delta sigma weight residual 114.92 106.75 8.17 1.30e+00 5.92e-01 3.95e+01 angle pdb=" N ASP B 88 " pdb=" CA ASP B 88 " pdb=" C ASP B 88 " ideal model delta sigma weight residual 114.62 107.56 7.06 1.14e+00 7.69e-01 3.84e+01 ... (remaining 29930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11983 17.95 - 35.90: 892 35.90 - 53.85: 136 53.85 - 71.79: 28 71.79 - 89.74: 18 Dihedral angle restraints: 13057 sinusoidal: 4744 harmonic: 8313 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 175.86 -82.86 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" C ALA D 75 " pdb=" N ALA D 75 " pdb=" CA ALA D 75 " pdb=" CB ALA D 75 " ideal model delta harmonic sigma weight residual -122.60 -141.40 18.80 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" N ALA D 75 " pdb=" C ALA D 75 " pdb=" CA ALA D 75 " pdb=" CB ALA D 75 " ideal model delta harmonic sigma weight residual 122.90 138.98 -16.08 0 2.50e+00 1.60e-01 4.14e+01 ... (remaining 13054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 3242 0.154 - 0.308: 249 0.308 - 0.462: 1 0.462 - 0.616: 0 0.616 - 0.769: 1 Chirality restraints: 3493 Sorted by residual: chirality pdb=" CA ALA D 75 " pdb=" N ALA D 75 " pdb=" C ALA D 75 " pdb=" CB ALA D 75 " both_signs ideal model delta sigma weight residual False 2.48 1.72 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA CYS C 361 " pdb=" N CYS C 361 " pdb=" C CYS C 361 " pdb=" CB CYS C 361 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA LEU A 212 " pdb=" N LEU A 212 " pdb=" C LEU A 212 " pdb=" CB LEU A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3490 not shown) Planarity restraints: 3891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 361 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C CYS C 361 " 0.062 2.00e-02 2.50e+03 pdb=" O CYS C 361 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL C 362 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 28 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C THR D 28 " 0.059 2.00e-02 2.50e+03 pdb=" O THR D 28 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE D 29 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 170 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C TYR B 170 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR B 170 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL B 171 " 0.017 2.00e-02 2.50e+03 ... (remaining 3888 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 809 2.69 - 3.25: 21174 3.25 - 3.80: 32869 3.80 - 4.35: 44141 4.35 - 4.90: 73412 Nonbonded interactions: 172405 Sorted by model distance: nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.161 2.440 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.169 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.176 2.440 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.186 2.440 ... (remaining 172400 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 27 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 93 or (resid 94 through 100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 101 through 107 or ( \ resid 108 through 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 119 or (resid 120 and (name N or name CA or name C or name O \ or name CB )) or resid 121 through 123 or (resid 124 through 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 133 or (resid 13 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 135 or (resi \ d 138 and (name N or name CA or name C or name O or name CB )) or resid 139 thro \ ugh 172 or (resid 186 through 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 204 or (resid 205 and (name N or name CA or name \ C or name O or name CB )) or resid 206 through 207 or (resid 208 and (name N or \ name CA or name C or name O or name CB )) or resid 209 through 217 or (resid 21 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 219 through \ 228 or (resid 229 and (name N or name CA or name C or name O or name CB )) or re \ sid 230 through 322 or (resid 323 through 324 and (name N or name CA or name C o \ r name O or name CB )) or resid 325 through 331 or (resid 332 through 335 and (n \ ame N or name CA or name C or name O or name CB )) or resid 336 through 339 or ( \ resid 340 through 342 and (name N or name CA or name C or name O or name CB )) o \ r resid 343 through 348 or (resid 349 through 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 356 or (resid 357 and (name N or \ name CA or name C or name O or name CB )) or resid 358 or (resid 359 through 36 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 361 through \ 363 or (resid 364 through 373 and (name N or name CA or name C or name O or name \ CB )) or resid 374 through 375 or (resid 376 through 378 and (name N or name CA \ or name C or name O or name CB )) or resid 379 or (resid 380 and (name N or nam \ e CA or name C or name O or name CB )) or resid 381 or (resid 382 through 383 an \ d (name N or name CA or name C or name O or name CB )) or resid 384 or (resid 38 \ 5 through 390 and (name N or name CA or name C or name O or name CB )) or resid \ 391 through 397 or (resid 398 through 403 and (name N or name CA or name C or na \ me O or name CB )) or (resid 404 through 411 and (name N or name CA or name C or \ name O or name CB )) or resid 412 through 413 or (resid 414 through 415 and (na \ me N or name CA or name C or name O or name CB )) or resid 416 or (resid 417 thr \ ough 425 and (name N or name CA or name C or name O or name CB )) or resid 426 t \ hrough 428 or (resid 429 through 430 and (name N or name CA or name C or name O \ or name CB )) or resid 431 through 432 or (resid 433 through 437 and (name N or \ name CA or name C or name O or name CB )) or resid 438 through 441 or resid 507 \ or (resid 508 through 520 and (name N or name CA or name C or name O or name CB \ )) or resid 521 through 522 or (resid 523 through 524 and (name N or name CA or \ name C or name O or name CB )) or resid 525 through 527 or (resid 528 through 53 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 532 through \ 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) or re \ sid 538 through 580 or (resid 581 and (name N or name CA or name C or name O or \ name CB )) or resid 582 or (resid 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 653 or (resid 654 and (name N or name CA or \ name C or name O or name CB )) or resid 655 through 744 or (resid 745 through 74 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 747 or (resi \ d 748 and (name N or name CA or name C or name O or name CB )) or resid 749 or ( \ resid 750 and (name N or name CA or name C or name O or name CB )) or resid 751 \ through 757 or (resid 758 and (name N or name CA or name C or name O or name CB \ )) or resid 759 through 785 or (resid 786 and (name N or name CA or name C or na \ me O or name CB )) or resid 787 through 810 or (resid 811 and (name N or name CA \ or name C or name O or name CB )) or resid 812 through 813 or (resid 814 and (n \ ame N or name CA or name C or name O or name CB )) or resid 815 through 936 or ( \ resid 937 and (name N or name CA or name C or name O or name CB )) or resid 938 \ or (resid 939 through 941 and (name N or name CA or name C or name O or name CB \ )) or resid 942 through 973 or (resid 974 and (name N or name CA or name C or na \ me O or name CB )) or resid 975 through 987 or (resid 988 through 989 and (name \ N or name CA or name C or name O or name CB )) or resid 990 through 1091 or (res \ id 1092 and (name N or name CA or name C or name O or name CB )) or resid 1093 t \ hrough 1126 or (resid 1127 and (name N or name CA or name C or name O or name CB \ )) or resid 1128 through 1141 or (resid 1142 and (name N or name CA or name C o \ r name O or name CB )) or resid 1143 through 1146)) selection = (chain 'C' and (resid 27 through 110 or resid 116 through 126 or (resid 127 thro \ ugh 129 and (name N or name CA or name C or name O or name CB )) or resid 130 th \ rough 135 or resid 138 through 141 or resid 166 through 236 or (resid 237 and (n \ ame N or name CA or name C or name O or name CB )) or resid 238 through 393 or ( \ resid 394 and (name N or name CA or name C or name O or name CB )) or resid 395 \ through 440 or (resid 441 and (name N or name CA or name C or name O or name CB \ )) or resid 507 through 555 or (resid 556 and (name N or name CA or name C or na \ me O or name CB )) or resid 557 or (resid 558 and (name N or name CA or name C o \ r name O or name CB )) or resid 559 through 567 or (resid 568 and (name N or nam \ e CA or name C or name O or name CB )) or resid 569 through 621 or resid 628 thr \ ough 631 or (resid 632 and (name N or name CA or name C or name O or name CB )) \ or resid 633 through 645 or (resid 646 through 647 and (name N or name CA or nam \ e C or name O or name CB )) or resid 648 through 809 or (resid 810 through 811 a \ nd (name N or name CA or name C or name O or name CB )) or resid 812 or (resid 8 \ 13 through 814 and (name N or name CA or name C or name O or name CB )) or resid \ 815 through 984 or (resid 985 and (name N or name CA or name C or name O or nam \ e CB )) or resid 986 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.620 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 56.450 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.011 0.057 21932 Z= 0.723 Angle : 1.153 14.385 29935 Z= 0.807 Chirality : 0.088 0.769 3493 Planarity : 0.007 0.052 3891 Dihedral : 13.099 89.742 7582 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.04 % Allowed : 1.43 % Favored : 98.52 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 2810 helix: 1.37 (0.21), residues: 653 sheet: -0.19 (0.21), residues: 614 loop : -1.57 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 116 HIS 0.006 0.001 HIS C1058 PHE 0.031 0.002 PHE D 112 TYR 0.020 0.003 TYR A 351 ARG 0.009 0.001 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.385 Fit side-chains REVERT: D 2 VAL cc_start: 0.3186 (OUTLIER) cc_final: 0.2962 (m) REVERT: A 54 LEU cc_start: 0.6578 (mm) cc_final: 0.6327 (tp) REVERT: A 92 PHE cc_start: 0.7562 (t80) cc_final: 0.7312 (t80) REVERT: A 754 LEU cc_start: 0.9269 (mt) cc_final: 0.9069 (mt) REVERT: B 541 PHE cc_start: 0.5959 (p90) cc_final: 0.5467 (p90) REVERT: B 867 ASP cc_start: 0.7584 (m-30) cc_final: 0.7342 (m-30) REVERT: B 979 ASP cc_start: 0.7253 (t0) cc_final: 0.7005 (t0) REVERT: C 266 TYR cc_start: 0.5916 (m-10) cc_final: 0.4907 (m-80) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.3032 time to fit residues: 84.1255 Evaluate side-chains 116 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 223 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 804 GLN B 935 GLN C 196 ASN C 784 GLN C 901 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21932 Z= 0.198 Angle : 0.564 8.376 29935 Z= 0.298 Chirality : 0.045 0.190 3493 Planarity : 0.005 0.053 3891 Dihedral : 4.789 33.280 3026 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.58 % Allowed : 5.95 % Favored : 93.46 % 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: -0.50 (0.16), residues: 2810 helix: 1.66 (0.21), residues: 663 sheet: -0.04 (0.20), residues: 629 loop : -1.42 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.002 0.001 HIS A 66 PHE 0.024 0.001 PHE B 318 TYR 0.023 0.001 TYR C1067 ARG 0.006 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 2.498 Fit side-chains REVERT: D 17 SER cc_start: 0.5922 (m) cc_final: 0.5532 (p) REVERT: A 54 LEU cc_start: 0.7133 (mm) cc_final: 0.6834 (tp) REVERT: A 92 PHE cc_start: 0.7473 (t80) cc_final: 0.7227 (t80) REVERT: A 754 LEU cc_start: 0.9196 (mt) cc_final: 0.8921 (mt) REVERT: B 541 PHE cc_start: 0.5903 (p90) cc_final: 0.5460 (p90) REVERT: B 979 ASP cc_start: 0.7146 (t0) cc_final: 0.6904 (t0) outliers start: 13 outliers final: 6 residues processed: 148 average time/residue: 0.3087 time to fit residues: 75.1783 Evaluate side-chains 122 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 215 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 259 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN C1088 HIS C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21932 Z= 0.165 Angle : 0.518 7.614 29935 Z= 0.272 Chirality : 0.044 0.174 3493 Planarity : 0.004 0.055 3891 Dihedral : 4.457 30.343 3025 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.98 % Allowed : 7.70 % Favored : 91.32 % 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: -0.34 (0.16), residues: 2810 helix: 1.90 (0.21), residues: 647 sheet: -0.04 (0.20), residues: 625 loop : -1.29 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.002 0.001 HIS C1088 PHE 0.013 0.001 PHE D 27 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 2.438 Fit side-chains REVERT: D 17 SER cc_start: 0.5995 (m) cc_final: 0.5481 (p) REVERT: D 18 LEU cc_start: 0.5517 (mp) cc_final: 0.4912 (mp) REVERT: A 54 LEU cc_start: 0.7116 (mm) cc_final: 0.6875 (tp) REVERT: A 92 PHE cc_start: 0.7358 (t80) cc_final: 0.7137 (t80) REVERT: A 400 PHE cc_start: 0.7974 (p90) cc_final: 0.7674 (p90) REVERT: A 754 LEU cc_start: 0.9160 (mt) cc_final: 0.8883 (mt) REVERT: B 541 PHE cc_start: 0.6068 (p90) cc_final: 0.5551 (p90) REVERT: B 979 ASP cc_start: 0.7305 (t0) cc_final: 0.7054 (t0) REVERT: C 86 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4851 (m-80) REVERT: C 201 PHE cc_start: 0.6622 (t80) cc_final: 0.6411 (t80) outliers start: 22 outliers final: 12 residues processed: 161 average time/residue: 0.3026 time to fit residues: 79.6807 Evaluate side-chains 136 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21932 Z= 0.244 Angle : 0.540 7.727 29935 Z= 0.283 Chirality : 0.044 0.168 3493 Planarity : 0.004 0.055 3891 Dihedral : 4.543 27.309 3025 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.52 % Allowed : 9.89 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2810 helix: 1.80 (0.21), residues: 651 sheet: -0.07 (0.20), residues: 621 loop : -1.26 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.003 0.001 HIS C1088 PHE 0.023 0.001 PHE C 192 TYR 0.023 0.001 TYR C1067 ARG 0.004 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 2.630 Fit side-chains REVERT: D 17 SER cc_start: 0.5833 (m) cc_final: 0.5335 (p) REVERT: A 54 LEU cc_start: 0.7201 (mm) cc_final: 0.6923 (tp) REVERT: A 92 PHE cc_start: 0.7300 (t80) cc_final: 0.7092 (t80) REVERT: A 754 LEU cc_start: 0.9196 (mt) cc_final: 0.8921 (mt) REVERT: B 541 PHE cc_start: 0.6156 (p90) cc_final: 0.5576 (p90) REVERT: B 979 ASP cc_start: 0.7346 (t0) cc_final: 0.7142 (t0) REVERT: C 86 PHE cc_start: 0.5339 (OUTLIER) cc_final: 0.4829 (m-80) REVERT: C 201 PHE cc_start: 0.6675 (t80) cc_final: 0.6474 (t80) outliers start: 34 outliers final: 20 residues processed: 156 average time/residue: 0.3085 time to fit residues: 78.9289 Evaluate side-chains 149 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 140 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 949 GLN C 282 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21932 Z= 0.209 Angle : 0.515 7.784 29935 Z= 0.270 Chirality : 0.044 0.164 3493 Planarity : 0.004 0.055 3891 Dihedral : 4.394 24.035 3025 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.52 % Allowed : 11.37 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2810 helix: 1.91 (0.21), residues: 651 sheet: -0.10 (0.20), residues: 612 loop : -1.20 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.003 0.001 HIS C 207 PHE 0.014 0.001 PHE B 306 TYR 0.021 0.001 TYR C1067 ARG 0.007 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 2.911 Fit side-chains revert: symmetry clash REVERT: D 17 SER cc_start: 0.5950 (m) cc_final: 0.5419 (p) REVERT: A 54 LEU cc_start: 0.7190 (mm) cc_final: 0.6873 (tp) REVERT: A 92 PHE cc_start: 0.7285 (t80) cc_final: 0.7073 (t80) REVERT: A 400 PHE cc_start: 0.8127 (p90) cc_final: 0.7824 (p90) REVERT: A 754 LEU cc_start: 0.9183 (mt) cc_final: 0.8900 (mt) REVERT: B 541 PHE cc_start: 0.6144 (p90) cc_final: 0.5544 (p90) REVERT: C 86 PHE cc_start: 0.5844 (OUTLIER) cc_final: 0.4928 (m-80) REVERT: C 105 ILE cc_start: 0.7832 (mt) cc_final: 0.7519 (tt) REVERT: C 902 MET cc_start: 0.8440 (tpp) cc_final: 0.8197 (tpp) outliers start: 34 outliers final: 20 residues processed: 164 average time/residue: 0.2905 time to fit residues: 79.3938 Evaluate side-chains 148 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 161 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 953 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21932 Z= 0.220 Angle : 0.524 7.737 29935 Z= 0.274 Chirality : 0.044 0.163 3493 Planarity : 0.004 0.055 3891 Dihedral : 4.369 22.860 3025 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.70 % Allowed : 11.91 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2810 helix: 1.86 (0.21), residues: 662 sheet: -0.05 (0.20), residues: 605 loop : -1.19 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.003 0.001 HIS C1088 PHE 0.017 0.001 PHE C 192 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 2.480 Fit side-chains revert: symmetry clash REVERT: D 17 SER cc_start: 0.6364 (m) cc_final: 0.5960 (p) REVERT: A 54 LEU cc_start: 0.7199 (mm) cc_final: 0.6877 (tp) REVERT: A 754 LEU cc_start: 0.9182 (mt) cc_final: 0.8879 (mt) REVERT: B 541 PHE cc_start: 0.6154 (p90) cc_final: 0.5553 (p90) REVERT: B 562 PHE cc_start: 0.6696 (p90) cc_final: 0.6422 (p90) REVERT: B 1138 TYR cc_start: 0.7529 (t80) cc_final: 0.7237 (t80) REVERT: C 86 PHE cc_start: 0.5489 (OUTLIER) cc_final: 0.4723 (m-80) outliers start: 38 outliers final: 30 residues processed: 159 average time/residue: 0.2946 time to fit residues: 77.9594 Evaluate side-chains 157 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 201 optimal weight: 30.0000 chunk 156 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21932 Z= 0.288 Angle : 0.561 6.947 29935 Z= 0.294 Chirality : 0.045 0.165 3493 Planarity : 0.004 0.056 3891 Dihedral : 4.549 23.401 3025 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.10 % Allowed : 11.86 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2810 helix: 1.81 (0.21), residues: 649 sheet: -0.22 (0.20), residues: 595 loop : -1.24 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.004 0.001 HIS C1088 PHE 0.018 0.002 PHE A 592 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 2.584 Fit side-chains REVERT: D 6 GLU cc_start: 0.5338 (OUTLIER) cc_final: 0.5050 (mm-30) REVERT: D 17 SER cc_start: 0.6517 (m) cc_final: 0.6000 (p) REVERT: A 54 LEU cc_start: 0.7252 (mm) cc_final: 0.6904 (tp) REVERT: A 400 PHE cc_start: 0.8050 (p90) cc_final: 0.7816 (p90) REVERT: A 754 LEU cc_start: 0.9201 (mt) cc_final: 0.8909 (mt) REVERT: A 1005 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7857 (mm-40) REVERT: B 1138 TYR cc_start: 0.7595 (t80) cc_final: 0.7284 (t80) REVERT: C 86 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.4712 (m-80) outliers start: 47 outliers final: 36 residues processed: 163 average time/residue: 0.2964 time to fit residues: 80.5717 Evaluate side-chains 161 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 174 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 21932 Z= 0.157 Angle : 0.501 6.905 29935 Z= 0.262 Chirality : 0.043 0.162 3493 Planarity : 0.004 0.055 3891 Dihedral : 4.177 20.176 3025 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.52 % Allowed : 12.89 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2810 helix: 2.03 (0.21), residues: 657 sheet: -0.08 (0.21), residues: 598 loop : -1.13 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 36 HIS 0.003 0.001 HIS C 207 PHE 0.016 0.001 PHE C 192 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 2.188 Fit side-chains REVERT: D 6 GLU cc_start: 0.5351 (OUTLIER) cc_final: 0.5012 (mm-30) REVERT: D 17 SER cc_start: 0.6438 (m) cc_final: 0.5993 (p) REVERT: A 54 LEU cc_start: 0.7187 (mm) cc_final: 0.6753 (tp) REVERT: A 106 PHE cc_start: 0.8011 (m-80) cc_final: 0.7594 (m-80) REVERT: A 754 LEU cc_start: 0.9143 (mt) cc_final: 0.8842 (mt) REVERT: A 902 MET cc_start: 0.8868 (tpp) cc_final: 0.8585 (tpp) REVERT: C 86 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5049 (m-80) outliers start: 34 outliers final: 25 residues processed: 168 average time/residue: 0.2972 time to fit residues: 82.1957 Evaluate side-chains 156 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 255 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 201 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 270 optimal weight: 7.9990 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21932 Z= 0.242 Angle : 0.534 7.375 29935 Z= 0.278 Chirality : 0.044 0.162 3493 Planarity : 0.004 0.056 3891 Dihedral : 4.317 22.939 3025 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.57 % Allowed : 13.12 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2810 helix: 1.89 (0.21), residues: 661 sheet: -0.10 (0.21), residues: 575 loop : -1.13 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.003 0.001 HIS C1088 PHE 0.015 0.001 PHE B 318 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 2.233 Fit side-chains REVERT: D 6 GLU cc_start: 0.5292 (OUTLIER) cc_final: 0.4978 (mm-30) REVERT: D 17 SER cc_start: 0.6606 (m) cc_final: 0.6199 (p) REVERT: A 54 LEU cc_start: 0.7225 (mm) cc_final: 0.6883 (tp) REVERT: A 754 LEU cc_start: 0.9179 (mt) cc_final: 0.8894 (mt) REVERT: A 1005 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7897 (mm-40) REVERT: C 86 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.4726 (m-80) outliers start: 35 outliers final: 29 residues processed: 154 average time/residue: 0.3047 time to fit residues: 77.3604 Evaluate side-chains 155 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 188 optimal weight: 0.9980 chunk 283 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 226 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21932 Z= 0.302 Angle : 0.565 6.977 29935 Z= 0.297 Chirality : 0.045 0.166 3493 Planarity : 0.004 0.057 3891 Dihedral : 4.565 23.547 3025 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.75 % Allowed : 12.98 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2810 helix: 1.76 (0.21), residues: 650 sheet: -0.20 (0.21), residues: 581 loop : -1.20 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS C1088 PHE 0.016 0.002 PHE C 238 TYR 0.023 0.002 TYR C1067 ARG 0.005 0.001 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 2.393 Fit side-chains REVERT: D 17 SER cc_start: 0.7318 (m) cc_final: 0.6887 (p) REVERT: A 54 LEU cc_start: 0.7257 (mm) cc_final: 0.6910 (tp) REVERT: A 754 LEU cc_start: 0.9196 (mt) cc_final: 0.8908 (mt) REVERT: A 902 MET cc_start: 0.8967 (tpp) cc_final: 0.8692 (tpp) REVERT: A 1005 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7887 (mm-40) REVERT: C 86 PHE cc_start: 0.5498 (OUTLIER) cc_final: 0.4728 (m-80) outliers start: 39 outliers final: 35 residues processed: 154 average time/residue: 0.2908 time to fit residues: 73.8143 Evaluate side-chains 160 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 226 optimal weight: 40.0000 chunk 94 optimal weight: 5.9990 chunk 232 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 198 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.119592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095492 restraints weight = 55816.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095194 restraints weight = 35489.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095672 restraints weight = 31538.882| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21932 Z= 0.261 Angle : 0.546 7.099 29935 Z= 0.286 Chirality : 0.044 0.160 3493 Planarity : 0.004 0.058 3891 Dihedral : 4.492 23.308 3025 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.84 % Allowed : 13.03 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2810 helix: 1.78 (0.21), residues: 650 sheet: -0.24 (0.21), residues: 588 loop : -1.21 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.003 0.001 HIS B 625 PHE 0.014 0.001 PHE C 906 TYR 0.022 0.001 TYR C1067 ARG 0.004 0.000 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3422.14 seconds wall clock time: 63 minutes 27.79 seconds (3807.79 seconds total)