Starting phenix.real_space_refine (version: dev) on Sun Feb 26 05:41:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qur_14152/02_2023/7qur_14152_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qur_14152/02_2023/7qur_14152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qur_14152/02_2023/7qur_14152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qur_14152/02_2023/7qur_14152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qur_14152/02_2023/7qur_14152_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qur_14152/02_2023/7qur_14152_updated.pdb" } resolution = 2.27 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= 0.006 sd= 0.135 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 Process input model Symmetric amino acids flipped Residue "A ASP 88": "OD1" <-> "OD2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27174 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 Chain: "B" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 Chain: "C" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 221 Unusual residues: {'EIC': 1, 'GE9': 1, 'NAG': 12, 'SIA': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 221 Unusual residues: {'EIC': 1, 'GE9': 1, 'NAG': 12, 'SIA': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 221 Unusual residues: {'EIC': 1, 'GE9': 1, 'NAG': 12, 'SIA': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 505 " occ=0.50 residue: pdb=" N ATYR B 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 505 " occ=0.50 residue: pdb=" N ATYR C 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 505 " occ=0.50 Time building chain proxies: 27.06, per 1000 atoms: 1.00 Number of scatterers: 27174 At special positions: 0 Unit cell: (141.04, 156.62, 167.28, 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) I 9 52.95 S 120 16.00 O 5565 8.00 N 4386 7.00 C 17094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " 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 A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " 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 C1032 " - pdb=" SG CYS C1043 " distance=2.03 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 Links applied BETA1-3 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 2 " " NAG O 1 " - " FUC O 2 " 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 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " " NAG K 1 " - " FUC K 4 " " NAG O 1 " - " FUC O 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 149 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 149 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 149 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " 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 A 165 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 165 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C 165 " Time building additional restraints: 11.75 Conformation dependent library (CDL) restraints added in 7.8 seconds 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6174 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 42 sheets defined 21.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.471A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 4.174A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.569A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 837 through 840 No H-bonds generated for 'chain 'A' and resid 837 through 840' Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 898 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 920 through 939 Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.932A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.837A 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 1032 removed outlier: 4.016A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.471A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 4.174A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.569A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 837 through 840 No H-bonds generated for 'chain 'B' and resid 837 through 840' Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 867 through 883 Processing helix chain 'B' and resid 887 through 890 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 920 through 939 Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.932A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.836A 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 1032 removed outlier: 4.015A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.472A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 4.174A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.569A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 837 through 840 No H-bonds generated for 'chain 'C' and resid 837 through 840' Processing helix chain 'C' and resid 843 through 847 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 887 through 890 Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 920 through 939 Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.933A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.836A 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 1032 removed outlier: 4.017A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.927A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.713A 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 56 removed outlier: 3.991A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.808A pdb=" N THR A 76 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.260A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.615A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= J, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= K, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.523A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.920A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.852A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.202A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 47 through 56 removed outlier: 3.991A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 67 through 70 removed outlier: 3.809A pdb=" N THR B 76 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.259A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.615A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= X, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= Y, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.524A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.920A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.851A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.202A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 47 through 56 removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 67 through 70 removed outlier: 3.809A pdb=" N THR C 76 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.259A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.615A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= AL, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AM, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.523A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.919A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.852A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.203A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2679 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: 12.16 Time building geometry restraints manager: 12.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.35: 8523 1.35 - 1.54: 18366 1.54 - 1.73: 444 1.73 - 1.92: 150 1.92 - 2.11: 9 Bond restraints: 27492 Sorted by residual: bond pdb=" C10 SIA C1315 " pdb=" N5 SIA C1315 " ideal model delta sigma weight residual 1.358 1.510 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C10 SIA B1314 " pdb=" N5 SIA B1314 " ideal model delta sigma weight residual 1.358 1.510 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C10 SIA A1314 " pdb=" N5 SIA A1314 " ideal model delta sigma weight residual 1.358 1.510 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C07 GE9 A1313 " pdb=" N01 GE9 A1313 " ideal model delta sigma weight residual 1.336 1.451 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C07 GE9 B1313 " pdb=" N01 GE9 B1313 " ideal model delta sigma weight residual 1.336 1.451 -0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 27487 not shown) Histogram of bond angle deviations from ideal: 100.14 - 110.62: 8449 110.62 - 121.10: 20919 121.10 - 131.58: 8009 131.58 - 142.05: 27 142.05 - 152.53: 3 Bond angle restraints: 37407 Sorted by residual: angle pdb=" C11 EIC A1315 " pdb=" C10 EIC A1315 " pdb=" C9 EIC A1315 " ideal model delta sigma weight residual 127.32 152.53 -25.21 3.00e+00 1.11e-01 7.06e+01 angle pdb=" C11 EIC B1315 " pdb=" C10 EIC B1315 " pdb=" C9 EIC B1315 " ideal model delta sigma weight residual 127.32 152.53 -25.21 3.00e+00 1.11e-01 7.06e+01 angle pdb=" C11 EIC C1301 " pdb=" C10 EIC C1301 " pdb=" C9 EIC C1301 " ideal model delta sigma weight residual 127.32 152.50 -25.18 3.00e+00 1.11e-01 7.04e+01 angle pdb=" C10 EIC A1315 " pdb=" C9 EIC A1315 " pdb=" C8 EIC A1315 " ideal model delta sigma weight residual 127.75 111.99 15.76 3.00e+00 1.11e-01 2.76e+01 angle pdb=" C10 EIC B1315 " pdb=" C9 EIC B1315 " pdb=" C8 EIC B1315 " ideal model delta sigma weight residual 127.75 112.00 15.75 3.00e+00 1.11e-01 2.75e+01 ... (remaining 37402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 14451 17.75 - 35.49: 1275 35.49 - 53.24: 348 53.24 - 70.99: 99 70.99 - 88.74: 30 Dihedral angle restraints: 16203 sinusoidal: 6573 harmonic: 9630 Sorted by residual: dihedral pdb=" CA VAL B 615 " pdb=" C VAL B 615 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta harmonic sigma weight residual 180.00 147.88 32.12 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA VAL A 615 " pdb=" C VAL A 615 " pdb=" N ASN A 616 " pdb=" CA ASN A 616 " ideal model delta harmonic sigma weight residual 180.00 147.88 32.12 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA VAL C 615 " pdb=" C VAL C 615 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta harmonic sigma weight residual 180.00 147.90 32.10 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 16200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4407 0.149 - 0.298: 3 0.298 - 0.447: 3 0.447 - 0.596: 0 0.596 - 0.745: 3 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 ... (remaining 4413 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO C 209 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " -0.049 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO B 209 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " -0.049 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO A 209 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " -0.041 5.00e-02 4.00e+02 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.71: 798 2.71 - 3.27: 26662 3.27 - 3.83: 49912 3.83 - 4.40: 64004 4.40 - 4.96: 104521 Nonbonded interactions: 245897 Sorted by model distance: nonbonded pdb=" OG1 THR C 645 " pdb=" O ARG C 646 " model vdw 2.145 2.440 nonbonded pdb=" OG1 THR A 645 " pdb=" O ARG A 646 " model vdw 2.146 2.440 nonbonded pdb=" OG1 THR B 645 " pdb=" O ARG B 646 " model vdw 2.146 2.440 nonbonded pdb=" OG1 THR A 676 " pdb=" OE1 GLN A 690 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR C 676 " pdb=" OE1 GLN C 690 " model vdw 2.202 2.440 ... (remaining 245892 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 504 or resid 506 through 877 or resid 879 throu \ gh 1139 or resid 1302 through 1312)) selection = (chain 'B' and (resid 14 through 504 or resid 506 through 877 or resid 879 throu \ gh 1139 or resid 1302 through 1312)) selection = (chain 'C' and (resid 14 through 504 or resid 506 through 877 or resid 879 throu \ gh 1139 or resid 1302 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 9 10.91 5 S 120 5.16 5 C 17094 2.51 5 N 4386 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.800 Check model and map are aligned: 0.390 Process input model: 89.710 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 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 : 0.004 0.152 27492 Z= 0.289 Angle : 0.623 25.213 37407 Z= 0.303 Chirality : 0.047 0.745 4416 Planarity : 0.004 0.075 4752 Dihedral : 15.547 88.735 9903 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.13 (0.14), residues: 3297 helix: 1.63 (0.20), residues: 705 sheet: 0.34 (0.19), residues: 738 loop : -0.97 (0.14), residues: 1854 *********************** 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 265 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 256 average time/residue: 1.3435 time to fit residues: 408.5689 Evaluate side-chains 219 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.3867 time to fit residues: 7.2645 ------------------------------------------------------------------------------- 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: 5.9990 chunk 250 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 258 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 334 ASN C 804 GLN C 957 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 27492 Z= 0.323 Angle : 0.595 7.462 37407 Z= 0.319 Chirality : 0.046 0.372 4416 Planarity : 0.005 0.075 4752 Dihedral : 6.462 63.111 4038 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.08 % Favored : 95.74 % Rotamer Outliers : 2.33 % 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: -0.26 (0.14), residues: 3297 helix: 1.40 (0.19), residues: 690 sheet: 0.32 (0.18), residues: 777 loop : -1.03 (0.14), residues: 1830 *********************** 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 277 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 210 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 29 residues processed: 261 average time/residue: 1.3172 time to fit residues: 411.9837 Evaluate side-chains 237 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 3.092 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 1.0143 time to fit residues: 14.5724 ------------------------------------------------------------------------------- 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: 5.9990 chunk 93 optimal weight: 2.9990 chunk 249 optimal weight: 0.4980 chunk 204 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 300 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 27492 Z= 0.306 Angle : 0.570 7.907 37407 Z= 0.307 Chirality : 0.045 0.380 4416 Planarity : 0.004 0.068 4752 Dihedral : 6.188 51.857 4038 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer Outliers : 1.88 % 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: -0.29 (0.14), residues: 3297 helix: 1.39 (0.19), residues: 684 sheet: 0.34 (0.18), residues: 777 loop : -1.07 (0.14), residues: 1836 *********************** 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 277 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 223 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 28 residues processed: 262 average time/residue: 1.2689 time to fit residues: 397.7827 Evaluate side-chains 240 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 3.237 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 6 average time/residue: 0.8493 time to fit residues: 10.7840 ------------------------------------------------------------------------------- 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: 0.5980 chunk 225 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 301 optimal weight: 0.5980 chunk 318 optimal weight: 3.9990 chunk 157 optimal weight: 0.0980 chunk 285 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN B 804 GLN C 493 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 27492 Z= 0.159 Angle : 0.492 5.413 37407 Z= 0.267 Chirality : 0.044 0.627 4416 Planarity : 0.004 0.063 4752 Dihedral : 5.513 39.007 4038 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.90 % Favored : 95.92 % Rotamer Outliers : 1.74 % 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: -0.20 (0.14), residues: 3297 helix: 1.54 (0.20), residues: 702 sheet: 0.30 (0.18), residues: 765 loop : -1.01 (0.14), residues: 1830 *********************** 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 278 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 228 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 21 residues processed: 261 average time/residue: 1.2667 time to fit residues: 397.9251 Evaluate side-chains 240 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 219 time to evaluate : 2.974 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.5302 time to fit residues: 7.0233 ------------------------------------------------------------------------------- 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: 6.9990 chunk 181 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 272 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 286 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 27492 Z= 0.377 Angle : 0.595 7.661 37407 Z= 0.320 Chirality : 0.048 0.560 4416 Planarity : 0.004 0.063 4752 Dihedral : 6.011 43.057 4038 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.17 % Favored : 95.65 % Rotamer Outliers : 1.67 % 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: -0.31 (0.14), residues: 3297 helix: 1.33 (0.19), residues: 687 sheet: 0.26 (0.18), residues: 804 loop : -1.05 (0.14), residues: 1806 *********************** 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 267 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 30 residues processed: 254 average time/residue: 1.3135 time to fit residues: 400.2916 Evaluate side-chains 242 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 3.147 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 6 average time/residue: 1.1677 time to fit residues: 12.7990 ------------------------------------------------------------------------------- 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: 3.9990 chunk 287 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 187 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN A 957 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 27492 Z= 0.260 Angle : 0.543 6.844 37407 Z= 0.293 Chirality : 0.046 0.475 4416 Planarity : 0.004 0.058 4752 Dihedral : 5.811 40.796 4038 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.74 % Favored : 96.07 % Rotamer Outliers : 1.60 % 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: -0.31 (0.14), residues: 3297 helix: 1.29 (0.19), residues: 702 sheet: 0.25 (0.18), residues: 801 loop : -1.05 (0.14), residues: 1794 *********************** 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 265 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 219 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 28 residues processed: 254 average time/residue: 1.2585 time to fit residues: 384.0291 Evaluate side-chains 242 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 3.002 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 5 average time/residue: 0.7150 time to fit residues: 8.9305 ------------------------------------------------------------------------------- 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: 5.9990 chunk 35 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 0.0770 chunk 178 optimal weight: 2.9990 chunk 318 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 27492 Z= 0.249 Angle : 0.536 7.933 37407 Z= 0.289 Chirality : 0.046 0.489 4416 Planarity : 0.004 0.057 4752 Dihedral : 5.719 40.005 4038 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Rotamer Outliers : 1.64 % 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: -0.31 (0.14), residues: 3297 helix: 1.31 (0.19), residues: 702 sheet: 0.23 (0.18), residues: 801 loop : -1.04 (0.14), residues: 1794 *********************** 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 267 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 33 residues processed: 256 average time/residue: 1.2490 time to fit residues: 387.2042 Evaluate side-chains 252 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 219 time to evaluate : 3.582 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 1.0113 time to fit residues: 14.4812 ------------------------------------------------------------------------------- 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: 1.9990 chunk 127 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 157 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 27492 Z= 0.214 Angle : 0.516 5.914 37407 Z= 0.280 Chirality : 0.045 0.542 4416 Planarity : 0.004 0.057 4752 Dihedral : 5.590 38.803 4038 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.74 % Favored : 96.07 % Rotamer Outliers : 1.53 % 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: -0.27 (0.14), residues: 3297 helix: 1.39 (0.19), residues: 702 sheet: 0.23 (0.18), residues: 801 loop : -1.02 (0.14), residues: 1794 *********************** 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 264 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 3.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 253 average time/residue: 1.3093 time to fit residues: 401.0973 Evaluate side-chains 241 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 3.358 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.8472 time to fit residues: 8.6383 ------------------------------------------------------------------------------- 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: 0.6980 chunk 304 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 296 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 267 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 27492 Z= 0.325 Angle : 0.575 7.264 37407 Z= 0.310 Chirality : 0.048 0.593 4416 Planarity : 0.004 0.057 4752 Dihedral : 5.858 40.681 4038 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.14 % Favored : 95.68 % Rotamer Outliers : 1.53 % 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: -0.35 (0.14), residues: 3297 helix: 1.31 (0.19), residues: 687 sheet: 0.22 (0.18), residues: 804 loop : -1.08 (0.14), residues: 1806 *********************** 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 265 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 30 residues processed: 253 average time/residue: 1.2946 time to fit residues: 393.1715 Evaluate side-chains 251 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 3.028 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.8316 time to fit residues: 9.7589 ------------------------------------------------------------------------------- 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: 0.9980 chunk 313 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 328 optimal weight: 4.9990 chunk 302 optimal weight: 0.0270 chunk 261 optimal weight: 0.1980 chunk 27 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 27492 Z= 0.169 Angle : 0.494 5.839 37407 Z= 0.268 Chirality : 0.045 0.545 4416 Planarity : 0.004 0.056 4752 Dihedral : 5.416 37.584 4038 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.87 % Favored : 95.95 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3297 helix: 1.44 (0.20), residues: 702 sheet: 0.22 (0.18), residues: 795 loop : -1.02 (0.14), residues: 1800 ********************** 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 255 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 226 time to evaluate : 3.093 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: 29 outliers final: 21 residues processed: 255 average time/residue: 1.2814 time to fit residues: 393.9008 Evaluate side-chains 243 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 3.143 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 4.4636 ------------------------------------------------------------------------------- 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: 2.9990 chunk 278 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1101 HIS C 493 GLN C 935 GLN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095564 restraints weight = 32459.348| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.25 r_work: 0.3051 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 27492 Z= 0.323 Angle : 0.570 7.083 37407 Z= 0.307 Chirality : 0.048 0.490 4416 Planarity : 0.004 0.057 4752 Dihedral : 5.768 40.062 4038 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.14 % Favored : 95.68 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3297 helix: 1.21 (0.19), residues: 705 sheet: 0.25 (0.18), residues: 801 loop : -1.06 (0.14), residues: 1791 =============================================================================== Job complete usr+sys time: 8879.50 seconds wall clock time: 160 minutes 40.54 seconds (9640.54 seconds total)