Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 01:38:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu2_33456/04_2023/7xu2_33456_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu2_33456/04_2023/7xu2_33456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu2_33456/04_2023/7xu2_33456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu2_33456/04_2023/7xu2_33456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu2_33456/04_2023/7xu2_33456_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu2_33456/04_2023/7xu2_33456_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17166 2.51 5 N 4413 2.21 5 O 5265 1.98 5 H 25248 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 52218 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 17063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 17063 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1054} Chain breaks: 3 Chain: "C" Number of atoms: 17063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 17063 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1054} Chain breaks: 3 Chain: "B" Number of atoms: 17063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 17063 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1054} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 17.68, per 1000 atoms: 0.34 Number of scatterers: 52218 At special positions: 0 Unit cell: (137.93, 152.784, 167.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 5265 8.00 N 4413 7.00 C 17166 6.00 H 25248 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS B 987 " distance=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS B 427 " 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 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 343 " " NAG A1312 " - " ASN A 17 " " NAG B1802 " - " ASN B 61 " " NAG B1803 " - " ASN B 122 " " NAG B1804 " - " ASN B 331 " " NAG B1805 " - " ASN B 616 " " NAG B1806 " - " ASN B 657 " " NAG B1807 " - " ASN B 709 " " NAG B1808 " - " ASN B1074 " " NAG B1809 " - " ASN B1098 " " NAG B1810 " - " ASN B 165 " " NAG B1811 " - " ASN B 282 " " NAG B1812 " - " ASN B 343 " " NAG B1813 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN C 234 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1134 " Time building additional restraints: 30.61 Conformation dependent library (CDL) restraints added in 3.6 seconds 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB VAL C 70 " pdb=" CB VAL B 70 " Number of C-beta restraints generated: 6212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 45 sheets defined 20.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.336A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 782 removed outlier: 4.746A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 914 through 917 No H-bonds generated for 'chain 'A' and resid 914 through 917' Processing helix chain 'A' and resid 920 through 940 removed outlier: 3.988A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.950A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1031 removed outlier: 5.421A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.336A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 631 through 634 No H-bonds generated for 'chain 'C' and resid 631 through 634' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 782 removed outlier: 4.737A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 909 Processing helix chain 'C' and resid 914 through 917 No H-bonds generated for 'chain 'C' and resid 914 through 917' Processing helix chain 'C' and resid 920 through 940 removed outlier: 3.979A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.962A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1031 removed outlier: 5.431A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.336A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 782 removed outlier: 4.753A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 914 through 917 No H-bonds generated for 'chain 'B' and resid 914 through 917' Processing helix chain 'B' and resid 920 through 940 removed outlier: 3.992A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.961A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1031 removed outlier: 5.427A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.067A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.104A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'A' and resid 311 through 314 Processing sheet with id= E, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.132A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= G, first strand: chain 'A' and resid 539 through 543 Processing sheet with id= H, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.445A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 692 through 696 removed outlier: 5.774A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 712 through 715 Processing sheet with id= K, first strand: chain 'A' and resid 718 through 728 Processing sheet with id= L, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= M, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id= O, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 6.963A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.043A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.116A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= S, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= T, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.129A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'C' and resid 539 through 543 Processing sheet with id= W, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.453A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 692 through 696 removed outlier: 5.775A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 712 through 715 Processing sheet with id= Z, first strand: chain 'C' and resid 718 through 728 Processing sheet with id= AA, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= AB, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AC, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id= AD, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 6.972A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.051A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.105A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= AH, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= AI, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.127A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= AK, first strand: chain 'B' and resid 539 through 543 Processing sheet with id= AL, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.442A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 692 through 696 removed outlier: 5.788A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 712 through 715 Processing sheet with id= AO, first strand: chain 'B' and resid 718 through 728 Processing sheet with id= AP, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= AQ, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AR, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id= AS, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 6.963A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2412 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: 17.08 Time building geometry restraints manager: 32.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 25242 1.05 - 1.26: 4359 1.26 - 1.48: 11457 1.48 - 1.69: 11610 1.69 - 1.91: 156 Bond restraints: 52824 Sorted by residual: bond pdb=" C4C BLA B1814 " pdb=" NC BLA B1814 " ideal model delta sigma weight residual 1.375 1.542 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C4C BLA C1313 " pdb=" NC BLA C1313 " ideal model delta sigma weight residual 1.375 1.542 -0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" C4C BLA A1313 " pdb=" NC BLA A1313 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" NB BLA B1814 " pdb=" C4B BLA B1814 " ideal model delta sigma weight residual 1.371 1.532 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" NB BLA C1313 " pdb=" C4B BLA C1313 " ideal model delta sigma weight residual 1.371 1.532 -0.161 2.00e-02 2.50e+03 6.49e+01 ... (remaining 52819 not shown) Histogram of bond angle deviations from ideal: 82.09 - 92.60: 8 92.60 - 103.10: 112 103.10 - 113.61: 62256 113.61 - 124.12: 29607 124.12 - 134.62: 2700 Bond angle restraints: 94683 Sorted by residual: angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 134.62 -20.22 2.30e+00 1.89e-01 7.73e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 134.48 -20.08 2.30e+00 1.89e-01 7.62e+01 angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 134.42 -20.02 2.30e+00 1.89e-01 7.57e+01 angle pdb=" CG2 THR C 95 " pdb=" CB THR C 95 " pdb=" HB THR C 95 " ideal model delta sigma weight residual 108.00 82.09 25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" OG1 THR C 95 " pdb=" CB THR C 95 " pdb=" HB THR C 95 " ideal model delta sigma weight residual 109.00 83.37 25.63 3.00e+00 1.11e-01 7.30e+01 ... (remaining 94678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 19378 17.53 - 35.06: 1481 35.06 - 52.59: 238 52.59 - 70.12: 74 70.12 - 87.65: 35 Dihedral angle restraints: 21206 sinusoidal: 9603 harmonic: 11603 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.58 48.42 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.84 48.16 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.92 48.08 1 1.00e+01 1.00e-02 3.19e+01 ... (remaining 21203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.544: 4392 0.544 - 1.087: 0 1.087 - 1.631: 1 1.631 - 2.174: 0 2.174 - 2.718: 2 Chirality restraints: 4395 Sorted by residual: chirality pdb=" CA VAL C 70 " pdb=" N VAL C 70 " pdb=" C VAL C 70 " pdb=" CB VAL C 70 " both_signs ideal model delta sigma weight residual False 2.44 -0.28 2.72 2.00e-01 2.50e+01 1.85e+02 chirality pdb=" CA VAL B 70 " pdb=" N VAL B 70 " pdb=" C VAL B 70 " pdb=" CB VAL B 70 " both_signs ideal model delta sigma weight residual False 2.44 -0.27 2.72 2.00e-01 2.50e+01 1.84e+02 chirality pdb=" CB THR C 95 " pdb=" CA THR C 95 " pdb=" OG1 THR C 95 " pdb=" CG2 THR C 95 " both_signs ideal model delta sigma weight residual False 2.55 1.00 1.55 2.00e-01 2.50e+01 6.02e+01 ... (remaining 4392 not shown) Planarity restraints: 7959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB BLA C1313 " 0.070 2.00e-02 2.50e+03 7.51e-02 1.41e+02 pdb=" OB BLA C1313 " -0.004 2.00e-02 2.50e+03 pdb=" C1B BLA C1313 " 0.072 2.00e-02 2.50e+03 pdb=" C2B BLA C1313 " 0.007 2.00e-02 2.50e+03 pdb=" C3B BLA C1313 " -0.019 2.00e-02 2.50e+03 pdb=" C4A BLA C1313 " -0.170 2.00e-02 2.50e+03 pdb=" C4B BLA C1313 " 0.014 2.00e-02 2.50e+03 pdb=" CAB BLA C1313 " -0.075 2.00e-02 2.50e+03 pdb=" CHB BLA C1313 " 0.105 2.00e-02 2.50e+03 pdb=" CMB BLA C1313 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA B1814 " 0.070 2.00e-02 2.50e+03 7.50e-02 1.40e+02 pdb=" OB BLA B1814 " -0.004 2.00e-02 2.50e+03 pdb=" C1B BLA B1814 " 0.072 2.00e-02 2.50e+03 pdb=" C2B BLA B1814 " 0.007 2.00e-02 2.50e+03 pdb=" C3B BLA B1814 " -0.019 2.00e-02 2.50e+03 pdb=" C4A BLA B1814 " -0.170 2.00e-02 2.50e+03 pdb=" C4B BLA B1814 " 0.013 2.00e-02 2.50e+03 pdb=" CAB BLA B1814 " -0.075 2.00e-02 2.50e+03 pdb=" CHB BLA B1814 " 0.106 2.00e-02 2.50e+03 pdb=" CMB BLA B1814 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA A1313 " 0.070 2.00e-02 2.50e+03 7.49e-02 1.40e+02 pdb=" OB BLA A1313 " -0.004 2.00e-02 2.50e+03 pdb=" C1B BLA A1313 " 0.072 2.00e-02 2.50e+03 pdb=" C2B BLA A1313 " 0.007 2.00e-02 2.50e+03 pdb=" C3B BLA A1313 " -0.018 2.00e-02 2.50e+03 pdb=" C4A BLA A1313 " -0.170 2.00e-02 2.50e+03 pdb=" C4B BLA A1313 " 0.013 2.00e-02 2.50e+03 pdb=" CAB BLA A1313 " -0.075 2.00e-02 2.50e+03 pdb=" CHB BLA A1313 " 0.105 2.00e-02 2.50e+03 pdb=" CMB BLA A1313 " 0.001 2.00e-02 2.50e+03 ... (remaining 7956 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 7709 2.27 - 2.85: 114825 2.85 - 3.44: 131054 3.44 - 4.02: 189275 4.02 - 4.60: 284797 Nonbonded interactions: 727660 Sorted by model distance: nonbonded pdb=" HG1 THR B 22 " pdb=" O THR B 76 " model vdw 1.689 1.850 nonbonded pdb=" HH TYR B 37 " pdb=" O LEU B 54 " model vdw 1.717 1.850 nonbonded pdb=" HH TYR A 37 " pdb=" O LEU A 54 " model vdw 1.721 1.850 nonbonded pdb=" HH TYR C 37 " pdb=" O LEU C 54 " model vdw 1.726 1.850 nonbonded pdb=" H LYS B 462 " pdb=" OE1 GLU B 465 " model vdw 1.727 1.850 ... (remaining 727655 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 14 through 1140 or resid 1302 through 1312)) selection = (chain 'B' and (resid 14 through 1140 or resid 1802 through 1812)) selection = (chain 'C' and (resid 14 through 1140 or resid 1302 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.590 Extract box with map and model: 12.270 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 118.130 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.167 27576 Z= 0.778 Angle : 0.952 20.223 37524 Z= 0.445 Chirality : 0.082 2.718 4395 Planarity : 0.004 0.075 4776 Dihedral : 13.930 87.646 9558 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3297 helix: 0.68 (0.19), residues: 744 sheet: -0.85 (0.17), residues: 768 loop : -1.66 (0.13), residues: 1785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 139 average time/residue: 0.7057 time to fit residues: 158.3319 Evaluate side-chains 104 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 3.111 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4796 time to fit residues: 12.6710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.6980 chunk 250 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 258 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 556 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 27576 Z= 0.293 Angle : 0.567 14.274 37524 Z= 0.289 Chirality : 0.062 1.707 4395 Planarity : 0.003 0.035 4776 Dihedral : 6.423 78.902 3648 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3297 helix: 1.10 (0.20), residues: 756 sheet: -0.57 (0.18), residues: 729 loop : -1.52 (0.13), residues: 1812 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 107 average time/residue: 0.7033 time to fit residues: 123.8547 Evaluate side-chains 101 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 3.126 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.7106 time to fit residues: 10.5964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 297 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 GLN A1101 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C1011 GLN C1101 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 27576 Z= 0.338 Angle : 0.567 14.703 37524 Z= 0.290 Chirality : 0.064 1.905 4395 Planarity : 0.003 0.032 4776 Dihedral : 6.152 63.031 3648 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.06 % 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: -0.96 (0.14), residues: 3297 helix: 1.16 (0.21), residues: 741 sheet: -0.45 (0.19), residues: 699 loop : -1.51 (0.13), residues: 1857 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 113 average time/residue: 0.6760 time to fit residues: 128.7912 Evaluate side-chains 100 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 3.122 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4846 time to fit residues: 10.2601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 0.6980 chunk 225 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN B 69 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 27576 Z= 0.288 Angle : 0.542 14.595 37524 Z= 0.277 Chirality : 0.062 1.816 4395 Planarity : 0.003 0.033 4776 Dihedral : 5.826 57.646 3648 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.06 % 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: -0.89 (0.14), residues: 3297 helix: 1.21 (0.20), residues: 744 sheet: -0.44 (0.18), residues: 711 loop : -1.45 (0.13), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 105 average time/residue: 0.7464 time to fit residues: 131.0721 Evaluate side-chains 96 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 3.097 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4897 time to fit residues: 6.7242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 27576 Z= 0.442 Angle : 0.591 15.243 37524 Z= 0.303 Chirality : 0.064 1.883 4395 Planarity : 0.003 0.036 4776 Dihedral : 5.994 59.928 3648 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3297 helix: 0.84 (0.20), residues: 780 sheet: -0.52 (0.18), residues: 762 loop : -1.51 (0.14), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 114 average time/residue: 0.6527 time to fit residues: 126.7397 Evaluate side-chains 103 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 3.109 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4610 time to fit residues: 13.5428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 27576 Z= 0.229 Angle : 0.537 14.449 37524 Z= 0.274 Chirality : 0.062 1.838 4395 Planarity : 0.003 0.034 4776 Dihedral : 5.807 57.257 3648 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.06 % 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: -0.92 (0.14), residues: 3297 helix: 1.13 (0.20), residues: 762 sheet: -0.58 (0.18), residues: 738 loop : -1.42 (0.13), residues: 1797 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 98 average time/residue: 0.7672 time to fit residues: 121.7710 Evaluate side-chains 94 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 3.114 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4921 time to fit residues: 5.7938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 180 optimal weight: 0.4980 chunk 268 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 27576 Z= 0.326 Angle : 0.552 14.640 37524 Z= 0.281 Chirality : 0.062 1.831 4395 Planarity : 0.003 0.035 4776 Dihedral : 5.801 58.423 3648 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3297 helix: 0.99 (0.20), residues: 780 sheet: -0.46 (0.18), residues: 762 loop : -1.42 (0.14), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 98 average time/residue: 0.7216 time to fit residues: 116.4167 Evaluate side-chains 94 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 3.150 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4717 time to fit residues: 7.6563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 27576 Z= 0.255 Angle : 0.531 14.387 37524 Z= 0.271 Chirality : 0.062 1.822 4395 Planarity : 0.003 0.034 4776 Dihedral : 5.668 59.797 3648 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.06 % 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: -0.86 (0.14), residues: 3297 helix: 1.06 (0.20), residues: 780 sheet: -0.51 (0.18), residues: 744 loop : -1.36 (0.14), residues: 1773 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 96 average time/residue: 0.7168 time to fit residues: 113.2063 Evaluate side-chains 95 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 3.129 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4907 time to fit residues: 8.4268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.4980 chunk 304 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 295 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 27576 Z= 0.252 Angle : 0.525 14.272 37524 Z= 0.268 Chirality : 0.062 1.817 4395 Planarity : 0.003 0.034 4776 Dihedral : 5.522 59.594 3648 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.06 % 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: -0.81 (0.14), residues: 3297 helix: 1.10 (0.20), residues: 780 sheet: -0.48 (0.18), residues: 744 loop : -1.33 (0.14), residues: 1773 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 95 average time/residue: 0.7232 time to fit residues: 112.9180 Evaluate side-chains 92 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 3.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4579 time to fit residues: 4.8385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 302 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 27576 Z= 0.247 Angle : 0.526 14.257 37524 Z= 0.268 Chirality : 0.062 1.814 4395 Planarity : 0.003 0.034 4776 Dihedral : 5.508 59.133 3648 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.06 % 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 (0.14), residues: 3297 helix: 1.12 (0.20), residues: 780 sheet: -0.42 (0.18), residues: 738 loop : -1.34 (0.14), residues: 1779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.8234 time to fit residues: 125.4687 Evaluate side-chains 92 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 4.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 241 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 269 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.069563 restraints weight = 148705.002| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.78 r_work: 0.2808 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 27576 Z= 0.161 Angle : 0.499 13.874 37524 Z= 0.254 Chirality : 0.062 1.809 4395 Planarity : 0.003 0.032 4776 Dihedral : 5.248 51.672 3648 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.06 % 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: -0.53 (0.14), residues: 3297 helix: 1.52 (0.21), residues: 744 sheet: -0.23 (0.19), residues: 711 loop : -1.23 (0.14), residues: 1842 =============================================================================== Job complete usr+sys time: 6411.16 seconds wall clock time: 113 minutes 25.48 seconds (6805.48 seconds total)